| 1. |
- Aquilante, Francesco, et al.
(författare)
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Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry
- 2017
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Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 115:17-18, s. 2052-2064
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Tidskriftsartikel (refereegranskat)abstract
- The density-fitting technique for approximating electron-repulsion integrals relies on the quality of auxiliary basis sets. These are commonly obtained through data fitting, an approach that presents some shortcomings. On the other hand, it is possible to derive auxiliary basis sets by removing elements from the product space of both contracted and primitive orbitals by means of a particular form of inner projection technique that has come to be known as Cholesky decomposition (CD). This procedure allows for on-the-fly construction of auxiliary basis sets that may be used in conjunction with any quantum chemical method, i.e. unbiased auxiliary basis sets. One key feature of these sets is that they represent the electron-repulsion integral matrix in atomic orbital basis with an accuracy that can be systematically improved. Another key feature is represented by the fact that locality of fitting coefficients is obtained even with the long-ranged Coulomb metric, as result of integral accuracy. Here we report on recent advances in the development of the CD-based density fitting technology. In particular, the implementation of analytical gradients algorithms is reviewed and the present status of local formulations - potentially linear scaling - is analysed in detail.
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| 2. |
- Aquilante, Francesco, et al.
(författare)
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Modern quantum chemistry with [Open]Molcas
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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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.
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| 3. |
- Aquilante, Francesco, et al.
(författare)
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Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table
- 2016
-
Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 506-541
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Tidskriftsartikel (refereegranskat)abstract
- In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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| 4. |
- Blachucki, Wojciech, et al.
(författare)
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Approaching the Attosecond Frontier of Dynamics in Matter with the Concept of X-ray Chronoscopy
- 2022
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Ingår i: Applied Sciences. - : MDPI AG. - 2076-3417. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- Featured Application Herein, an innovative methodology, called X-ray chronoscopy, is proposed for exploration of ultrafast processes in matter with attosecond precision using current XFEL sources. The method is based on measuring the change in an X-ray pulse temporal profile induced by interaction with a medium. X-ray free electron lasers (XFELs) have provided scientists opportunities to study matter with unprecedented temporal and spatial resolutions. However, access to the attosecond domain (i.e., below 1 femtosecond) remains elusive. Herein, a time-dependent experimental concept is theorized, allowing us to track ultrafast processes in matter with sub-fs resolution. The proposed X-ray chronoscopy approach exploits the state-of-the-art developments in terahertz streaking to measure the time structure of X-ray pulses with ultrahigh temporal resolution. The sub-femtosecond dynamics of the saturable X-ray absorption process is simulated. The employed rate equation model confirms that the X-ray-induced mechanisms leading to X-ray transparency can be probed via measurement of an X-ray pulse time structure.
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| 5. |
- Boström, Jonas, et al.
(författare)
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Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies
- 2010
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 6:3, s. 747-754
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Tidskriftsartikel (refereegranskat)abstract
- The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.
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| 6. |
- Chaudret, Robin, et al.
(författare)
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Revisiting H2O Nucleation around Au+ and Hg2+ : The Peculiar "Pseudo-Soft" Character of the Gold Cation
- 2014
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:5, s. 1900-1909
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Tidskriftsartikel (refereegranskat)abstract
- In this contribution, we propose a deeper understanding of the electronic effects affecting the nucleation of water around the Au+ and Hg2+ metal cations using quantum chemistry. To do so, and in order to go beyond usual energetical studies, we make extensive use of state of the art quantum interpretative techniques combining ELF/NCI/QTAIM/EDA computations to capture all ranges of interactions stabilizing the well characterized microhydrated structures. The Electron Localization Function (ELF) topological analysis reveals the peculiar role of the Au+ outer-shell core electrons (subvalence) that appear already spatially preorganized once the addition of the first water molecule occurs. Thus, despite the addition of other water molecules, the electronic structure of Au(H2O)(+) appears frozen due to relativistic effects leading to a maximal acceptation of only two waters in gold's first hydration shell. As the values of the QTAIM (Quantum Theory of Atoms in Molecules) cations's charge is discussed, the Non Covalent Interactions (NCI) analysis showed that Au+ appears still able to interact through longer range van der Waals interaction with the third or fourth hydration shell water molecules. As these types of interaction are not characteristic of either a hard or soft metal cation, we introduced the concept of a "pseudo-soft" cation to define Au+ behavior. Then, extending the study, we performed the same computations replacing Au+ with Hg2+, an isoelectronic cation. If Hg2+ behaves like Au+ for small water clusters, a topological, geometrical, and energetical transition appears when the number of water molecules increases. Regarding the HSAB theory, this transition is characteristic of a shift of Hg2+ from a pseudosoft form to a soft ion and appears to be due to a competition between the relativistic and correlation effects. Indeed, if relativistic effects are predominant, then mercury will behave like gold and have a similar subvalence/geometry; otherwise when correlation effects are predominant, Hg2+ behaves like a soft cation.
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| 7. |
- De Gracia Triviño, Juan Angel, et al.
(författare)
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Complete Active Space Methods for NISQ Devices: The Importance of Canonical Orbital Optimization for Accuracy and Noise Resilience
- 2023
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:10, s. 2863-2872
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Tidskriftsartikel (refereegranskat)abstract
- To avoid the scaling of the number of qubits with the size of the basis set, one can divide the molecular space into active and inactive regions, which is also known as complete active space methods. However, selecting the active space alone is not enough to accurately describe quantum mechanical effects such as correlation. This study emphasizes the importance of optimizing the active space orbitals to describe correlation and improve the basis-dependent Hartree-Fock energies. We will explore classical and quantum computation methods for orbital optimization and compare the chemically inspired ansatz, UCCSD, with the classical full CI approach for describing the active space in both weakly and strongly correlated molecules. Finally, we will investigate the practical implementation of a quantum CASSCF, where hardware-efficient circuits must be used and noise can interfere with accuracy and convergence. Additionally, we will examine the impact of using canonical and noncanonical active orbitals on the convergence of the quantum CASSCF routine in the presence of noise.
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| 8. |
- Delcey, Mickaël G., 1988-, et al.
(författare)
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Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase
- 2014
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 16:17, s. 7927-7938
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the geometry and singlet-triplet energy difference of two mono-nuclear Ni2+ models related to the active site in [NiFe] hydrogenase. Multiconfigurational second-order perturbation theory based on a complete active-space wavefunction with an active space of 12 electrons in 12 orbitals, CASPT2(12,12), reproduces experimental bond lengths to within 1 pm. Calculated singlet-triplet energy differences agree with those obtained from coupled-cluster calculations with single, double and (perturbatively treated) triple excitations (CCSD(T)) to within 12 kJ mol(-1). For a bimetallic model of the active site of [NiFe] hydrogenase, the CASPT2(12,12) results were compared with the results obtained with an extended active space of 22 electrons in 22 orbitals. This is so large that we need to use restricted active-space theory (RASPT2). The calculations predict that the singlet state is 48-57 kJ mol(-1) more stable than the triplet state for this model of the Ni-Sl(a) state. However, in the [NiFe] hydrogenase protein, the structure around the Ni ion is far from the square-planar structure preferred by the singlet state. This destabilises the singlet state so that it is only similar to 24 kJ mol(-1) more stable than the triplet state. Finally, we have studied how various density functional theory methods compare to the experimental, CCSD(T), CASPT2, and RASPT2 results. Semi-local functionals predict the best singlet-triplet energy differences, with BP86, TPSS, and PBE giving mean unsigned errors of 12-13 kJ mol(-1) (maximum errors of 25-31 kJ mol(-1)) compared to CCSD(T). For bond lengths, several methods give good results, e. g. TPSS, BP86, and M06, with mean unsigned errors of 2 pm for the bond lengths if relativistic effects are considered.
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| 9. |
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| 10. |
- Delcey, Mickaël G., 1988-, et al.
(författare)
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Analytical gradients of complete active space self-consistent field energies using Cholesky decomposition : Geometry optimization and spin-state energetics of a ruthenium nitrosyl complex
- 2014
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 140:17, s. 174103-
-
Tidskriftsartikel (refereegranskat)abstract
- We present a formulation of analytical energy gradients at the complete active space self-consistent field (CASSCF) level of theory employing density fitting (DF) techniques to enable efficient geometry optimizations of large systems. As an example, the ground and lowest triplet state geometries of a ruthenium nitrosyl complex are computed at the DF-CASSCF level of theory and compared with structures obtained from density functional theory (DFT) using the B3LYP, BP86, and M06L functionals. The average deviation of all bond lengths compared to the crystal structure is 0.042 angstrom at the DF-CASSCF level of theory, which is slightly larger but still comparable with the deviations obtained by the tested DFT functionals, e. g., 0.032 angstrom with M06L. Specifically, the root-mean-square deviation between the DF-CASSCF and best DFT coordinates, delivered by BP86, is only 0.08 angstrom for S-0 and 0.11 angstrom for T-1, indicating that the geometries are very similar. While keeping the mean energy gradient errors below 0.25%, the DF technique results in a 13-fold speedup compared to the conventional CASSCF geometry optimization algorithm. Additionally, we assess the singlet-triplet energy vertical and adiabatic differences with multiconfigurational second-order perturbation theory (CASPT2) using the DF-CASSCF and DFT optimized geometries. It is found that the vertical CASPT2 energies are relatively similar regardless of the geometry employed whereas the adiabatic singlet-triplet gaps are more sensitive to the chosen triplet geometry. (C) 2014 AIP Publishing LLC.
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| 11. |
- Delcey, Mickaël G., 1988-, et al.
(författare)
-
Analytical gradients of the state-average complete active space self-consistent field method with density fitting
- 2015
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 143:4
-
Tidskriftsartikel (refereegranskat)abstract
- An efficient implementation of the state-averaged complete active space self-consistent field (SA-CASSCF) gradients employing density fitting (DF) is presented. The DF allows a reduction both in scaling and prefactors of the different steps involved. The performance of the algorithm is demonstrated on a set of molecules ranging up to an iron-Heme b complex which with its 79 atoms and 811 basis functions is to our knowledge the largest SA-CASSCF gradient computed. For smaller systems where the conventional code could still be used as a reference, both the linear response calculation and the gradient formation showed a clear timing reduction and the overall cost of a geometry optimization is typically reduced by more than one order of magnitude while the accuracy loss is negligible.
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| 12. |
- Delcey, Mickaël G., 1988-, et al.
(författare)
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Communication : Theoretical prediction of the structure and spectroscopic properties of the X∼ and A∼ states of hydroxymethyl peroxy (HOCH2OO) radical
- 2013
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 138:2, s. 021105-
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Tidskriftsartikel (refereegranskat)abstract
- The hydroxymethyl peroxy (HMOO) radical is a radical product from the oxidation of non-methane hydrocarbons. The present study provides theoretical prediction of critical spectroscopic features of this radical that should aid in its experimental characterization. Structure, rotational constants, and harmonic frequencies are presented for the ground and first excited electronic states of HMOO. The adiabatic transition energy for the A←X process is 7360 cm-1, suggesting that this transition, occurring in the mid to near infrared, is the most promising candidate for observing the radical spectroscopically. The band origin of the A←X transition of HMOO is calibrated and benchmarked with the corresponding state of the HOO radical, which is experimentally and theoretically well characterized.
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| 13. |
- Delcey, Mickael G, et al.
(författare)
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Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions
- 2019
-
Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 40:19, s. 1789-1799
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Tidskriftsartikel (refereegranskat)abstract
- Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies.
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| 14. |
- Delcey, Mickael G., et al.
(författare)
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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.
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| 15. |
- Delcey, Mickaël G., 1988-
(författare)
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Extending the Reach of Accurate Wavefunction Methods
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Multiconfigurational quantum chemistry methods, and especially the multiconfigurational self-consistent field (MCSCF) and multireference perturbation theory (MRPT2), are powerful tools, particularly suited to the accurate modeling of photochemical processes and transition metal catalysis. However, they are limited by their high computational cost compared to other methods, especially density functional theory. Moreover, there are areas where they would be expected to perform well, but where they are not applied due to lack of experience.This thesis addresses those issues. First, the efficiency of the Cholesky decomposition approximation to reduce the cost of MCSCF and MRPT2 without sacrificing their accuracy is demonstrated. This then motivates the extension of the Cholesky approximation to the computation of MCSCF nuclear gradients, thus strongly improving the ability to perform MCSCF non-adiabatic molecular dynamics. Typically, a tenfold speed-up is observed allowing dynamic simulation of larger systems or over longer times.Finally, multiconfigurational methods are applied to the computation of X-ray spectra of transition metal complexes. The importance of the different parameters in the calculation is systematically investigated, laying the base for wider applications of those accurate methods in the modeling of X-ray spectroscopy. A tool to analyze the resulting spectrum in terms of molecular orbitals is also presented, strengthening the interplay between theory and experiments.With these developments and other significant ones that have happened in recent years, multiconfigurational methods can now reach new grounds and contribute to important new discoveries
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| 16. |
- Delcey, Mickaël G.
(författare)
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MultiPsi : A python-driven MCSCF program for photochemistry and spectroscopy simulations on modern HPC environments
- 2023
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Ingår i: Wiley Interdisciplinary Reviews: Computational Molecular Science. - 1759-0876. ; 13:6
-
Tidskriftsartikel (refereegranskat)abstract
- We present MultiPsi, an open-source MCSCF program for the calculation of ground and excited states properties of strongly correlated systems. The program currently implements a general MCSCF code with excited states available using either state-averaging or linear response. It is written in a highly modular fashion using Python/C++ which makes it well suited as a development platform, enabling easy prototyping of novel methods, and as a teaching tool using interactive notebooks. The code is also very efficient and designed for modern high-performance computing environments using hybrid OpenMP/MPI parallelization. This efficiency is demonstrated with the calculation of the CASSCF energy and linear response of a molecule with more than 700 atoms as well as a fully optimized conventional CI calculation on more than 400 billion determinants. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
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| 17. |
- Delcey, Mickael G, 1988-
(författare)
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MultiPsi: A python-driven MCSCF program for photochemistry and spectroscopy simulations on modern HPC environments
- 2023
-
Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 13:6
-
Tidskriftsartikel (refereegranskat)abstract
- We present MultiPsi, an open-source MCSCF program for the calculation of ground and excited states properties of strongly correlated systems. The program currently implements a general MCSCF code with excited states available using either state-averaging or linear response. It is written in a highly modular fashion using Python/C++ which makes it well suited as a development platform, enabling easy prototyping of novel methods, and as a teaching tool using interactive notebooks. The code is also very efficient and designed for modern high-performance computing environments using hybrid OpenMP/MPI parallelization. This efficiency is demonstrated with the calculation of the CASSCF energy and linear response of a molecule with more than 700 atoms as well as a fully optimized conventional CI calculation on more than 400 billion determinants. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
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| 18. |
- Delcey, Mickael G, 1988-, et al.
(författare)
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Soft X-ray signatures of cationic manganese–oxo systems, including a high-spin manganese(v) complex
- 2022
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:6, s. 3598-3610
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Tidskriftsartikel (refereegranskat)abstract
- Limitations in synthesis of high-valent metal–oxo complexes are circumvented by trapping a series of ionic Mn–oxo complexes. One of them is a rare high-spin Mn(v)–oxo, which can serve as a template to identify similar intermediates in catalysis.
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| 19. |
- Fernández Galván, Ignacio, et al.
(författare)
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Analytical State-Average Complete-Active-Space Self-Consistent Field Nonadiabatic Coupling Vectors : Implementation with Density-Fitted Two-Electron Integrals and Application to Conical Intersections
- 2016
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:8, s. 3636-3653
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Tidskriftsartikel (refereegranskat)abstract
- Analytical state-average complete-active-space self-consistent field derivative (nonadiabatic) coupling vectors are implemented. Existing formulations are modified such that the implementation is compatible with Cholesky-based density fitting of two-electron integrals, which results in efficient calculations especially with large basis sets. Using analytical nonadiabatic coupling vectors, the optimization of conical intersections is implemented within the projected constrained optimization method. The standard description and characterization of conical intersections is reviewed and clarified, and a practical and unambiguous system for their classification and interpretation is put forward. These new tools are subsequently tested and benchmarked for 19 different conical intersections. The accuracy of the derivative coupling vectors is validated, and the information that can be drawn from the proposed characterization is discussed, demonstrating its usefulness.
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| 20. |
- Fransson, Thomas, et al.
(författare)
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Computational Chemistry from Laptop to HPC : A notebook exploration of quantum chemistry
- 2022. - 1
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- Quantum chemistry is a powerful tool. It is now possible to model complex chemical processes even on a laptop getting insights into matter at its fundamental scale.But quantum chemistry is also very complex. Answering a chemical question requires selecting parameters among a wide variety of choices. Choosing a model system, an electronic structure method, a basis set, a set of properties, and a wide array of parameters which can affect the results in small but sometimes meaningful way… It can be a very daunting task, even for veterans of the field.Similarly, for those who wish to get a deeper understanding of a method, going through the pages of equation often riddled with inconsistent notations and formulations is very challenging. And at the end, the link between the equation and the computer implementation found in existing softwares can be vague at best.We believe that a core issue is that humans are not good at learning in abstract terms. We can get very far with a lecture or a textbook, but we will never build as much intuition about how a clock work as by simply breaking one apart and rebuilding it from scratch.This is exactly the aim of this page, allowing a hands-on approach to computational chemistry. Together we will dismantle the black box that a computational chemistry code often seems to be, go through all the cogs and gears, and build back together some of the main computational methods of modern computational chemistry. We will do this by presenting the underlying equations, all expressed with consistent notations, as well as by suggesting a simple python implementation, to really display in action how the theory is implemented into a practical tool. Additionally, we will put these methods in context by showing how they can be used to address concrete chemical questions, discussing the strengths and weaknesses of each method and how to best use them to solve practical problems.
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| 21. |
- Fransson, Thomas, et al.
(författare)
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eChem : A Notebook Exploration of Quantum Chemistry
- 2023
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Ingår i: Journal of Chemical Education. - : American Chemical Society (ACS). - 0021-9584 .- 1938-1328. ; 100:4, s. 1664-1671
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Tidskriftsartikel (refereegranskat)abstract
- The eChem project features an e-book published as a web page (10.30746/978-91-988114-0-7), collecting a repository of Jupyter notebooks developed for the dual purpose of explaining and exploring the theory underlying computational chemistry in a highly interactive manner as well as providing a tutorial-based presentation of the complex workflows needed to simulate embedded molecular systems of real biochemical and/or technical interest. For students ranging from beginners to advanced users, the eChem book is well suited for self-directed learning, but workshops led by experienced instructors and targeting student bodies with specific needs and interests can readily be formed from its components. This has been done by using eChem as the base for a workshop directed toward graduate students learning the theory and practices of quantum chemistry, resulting in very positive assessment of the interactive nature of this framework. The members of the eChem team are engaged in both education and research, and as a mirroring activity, we develop the open-source software upon which this e-book is predominantly based. The overarching vision and goal of our work is to provide a science- and education-enabling software platform for quantum molecular modeling on contemporary and future high-performance computing systems, and to document the resulting development and workflows in the eChem book.
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| 22. |
- Freitag, Leon, et al.
(författare)
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Orbital entanglement and CASSCF analysis of the Ru-NO bond in a Ruthenium nitrosyl complex
- 2015
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 17:22, s. 14383-14392
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Tidskriftsartikel (refereegranskat)abstract
- Complete active space self-consistent field (CASSCF) wavefunctions and an orbital entanglement analysis obtained from a density-matrix renormalisation group (DMRG) calculation are used to understand the electronic structure, and, in particular, the Ru-NO bond of a Ru nitrosyl complex. Based on the configurations and orbital occupation numbers obtained for the CASSCF wavefunction and on the orbital entropy measurements evaluated for the DMRG wavefunction, we unravel electron correlation effects in the Ru coordination sphere of the complex. It is shown that Ru-NO pi bonds show static and dynamic correlation, while other Ru-ligand bonds feature predominantly dynamic correlation. The presence of static correlation requires the use of multiconfigurational methods to describe the Ru-NO bond. Subsequently, the CASSCF wavefunction is analysed in terms of configuration state functions based on localised orbitals. The analysis of the wavefunctions in the electronic singlet ground state and the first triplet state provides a picture of the Ru-NO moiety beyond the standard representation based on formal oxidation states. A distinct description of the Ru and NO fragments is advocated. The electron configuration of Ru is an equally weighted superposition of Ru-II and Ru-III configurations, with the Ru-III configuration originating from charge donation mostly from Cl ligands. However, and contrary to what is typically assumed, the electronic configuration of the NO ligand is best described as electroneutral.
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| 23. |
- Galván, Ignacio Fdez., et al.
(författare)
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OpenMolcas : From Source Code to Insight
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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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.
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| 24. |
- Guo, Meiyuan, et al.
(författare)
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Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering
- 2016
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 120:29, s. 5848-5855
-
Tidskriftsartikel (refereegranskat)abstract
- For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s -> 3d) excitation can be followed by monitoring the dipole-allowed K alpha (2p -> 1s) or K beta (3p -> 1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)(6)](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)(6)](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems.
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| 25. |
- Guo, Meiyuan, et al.
(författare)
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Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method
- 2016
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 4, s. 3250-3259
-
Tidskriftsartikel (refereegranskat)abstract
- The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.
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| 26. |
- Kamerlin, Natasha, et al.
(författare)
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Toward a Computational Ecotoxicity Assay
- 2020
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Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 60:8, s. 3792-3803
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Tidskriftsartikel (refereegranskat)abstract
- Thousands of anthropogenic chemicals are released into the environment each year, posing potential hazards to human and environmental health. Toxic chemicals may cause a variety of adverse health effects, triggering immediate symptoms or delayed effects over longer periods of time. It is thus crucial to develop methods that can rapidly screen and predict the toxicity of chemicals to limit the potential harmful impacts of chemical pollutants. Computational methods are being increasingly used in toxicity predictions. Here, the method of molecular docking is assessed for screening potential toxicity of a variety of xenobiotic compounds, including pesticides, pharmaceuticals, pollutants, and toxins derived from the chemical industry. The method predicts the binding energy of pollutants to a set of carefully selected receptors under the assumption that toxicity in many cases is related to interference with biochemical pathways. The strength of the applied method lies in its rapid generation of interaction maps between potential toxins and the targeted enzymes, which could quickly yield molecular-level information and insight into potential perturbation pathways, aiding in the prioritization of chemicals for further tests. Two scoring functions are compared: Autodock Vina and the machine-learning scoring function RF-Score-VS. The results are promising, although hampered by the accuracy of the scoring functions. The strengths and weaknesses of the docking protocol are discussed, as well as future directions for improving the accuracy for the purpose of toxicity predictions.
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| 27. |
- Kamerlin, Natasha, et al.
(författare)
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Unravelling the mechanism of pH-regulation in dinoflagellate luciferase
- 2020
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Ingår i: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 164, s. 2671-2680
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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.
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| 28. |
- Kayser, Yves, et al.
(författare)
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Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses
- 2019
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.
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| 29. |
- Kunnus, Kristjan, et al.
(författare)
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Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering
- 2020
-
Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- The non-equilibrium dynamics of electrons and nuclei govern the function of photoactive materials. Disentangling these dynamics remains a critical goal for understanding photoactive materials. Here we investigate the photoinduced dynamics of the [Fe(bmip)2]2+ photosensitizer, where bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, with simultaneous femtosecond-resolution Fe Kα and Kβ X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS). This measurement shows temporal oscillations in the XES and XSS difference signals with the same 278 fs period oscillation. These oscillations originate from an Fe-ligand stretching vibrational wavepacket on a triplet metal-centered (3MC) excited state surface. This 3MC state is populated with a 110 fs time constant by 40% of the excited molecules while the rest relax to a 3MLCT excited state. The sensitivity of the Kα XES to molecular structure results from a 0.7% average Fe-ligand bond length shift between the 1 s and 2p core-ionized states surfaces.
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| 30. |
- Kunnus, Kristjan, et al.
(författare)
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Viewing the Valence Electronic Structure of Ferric and Ferrous Hexacyanide in Solution from the Fe and Cyanide Perspectives
- 2016
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 120:29, s. 7182-7194
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Tidskriftsartikel (refereegranskat)abstract
- The valence-excited states of ferric and ferrous hexacyanide ions in aqueous solution were mapped by resonant inelastic X-ray scattering (RIXS) at the Fe L-2,L-3 and N K edges. Probing of both the central Fe and the ligand N atoms enabled identification of the metal-and ligand-centered excited states, as well as ligand-to-metal and metal-to-ligand charge-transfer excited states. Ab initio calculations utilizing the RASPT2 method were used to simulate the Fe L-2,L-3-edge RIXS spectra and enabled quantification of the covalencies of both occupied and empty orbitals of pi and sigma symmetry. We found that pi back-donation in the ferric complex is smaller than that in the ferrous complex. This is evidenced by the relative amounts of Fe 3d character in the nominally 2 pi CN- molecular orbital of 7% and 9% in ferric and ferrous hexacyanide, respectively. Utilizing the direct sensitivity of Fe L-3-edge RIXS to the Fe 3d character in the occupied molecular orbitals, we also found that the donation interactions are dominated by sigma bonding. The latter was found to be stronger in the ferric complex, with an Fe 3d contribution to the nominally 5 sigma CN- molecular orbitals of 29% compared to 20% in the ferrous complex. These results are consistent with the notion that a higher charge at the central metal atom increases donation and decreases back-donation.
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| 31. |
- Källman, Erik, PhD, et al.
(författare)
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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
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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.
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| 32. |
- Källman, Erik, PhD, et al.
(författare)
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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
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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.
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| 33. |
- Lundberg, Marcus, 1974-, et al.
(författare)
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Multiconfigurational Approach to X-ray Spectroscopy of Transition Metal Complexes
- 2019
-
Ingår i: Transition Metals in Coordination Environments. - Cham : Springer. - 9783030117139 - 9783030117146 ; , s. 185-217
-
Bokkapitel (refereegranskat)abstract
- Close correlation between theoretical modeling and experimental spectroscopy allows for identification of the electronic and geometric structure of a system through its spectral fingerprint. This is can be used to verify mechanistic proposals and is a valuable complement to calculations of reaction mechanisms using the total energy as the main criterion. For transition metal systems, X-ray spectroscopy offers a unique probe because the core-excitation energies are element specific, which makes it possible to focus on the catalytic metal. The core hole is atom-centered and sensitive to the local changes in the electronic structure, making it useful for redox active catalysts. The possibility to do time-resolved experiments also allows for rapid detection of metastable intermediates. Reliable fingerprinting requires a theoretical model that is accurate enough to distinguish between different species and multiconfigurational wavefunction approaches have recently been extended to model a number of X-ray processes of transition metal complexes. Compared to ground-state calculations, modeling of X-ray spectra is complicated by the presence of the core hole, which typically leads to multiple open shells and large effects of spin–orbit coupling. This chapter describes how these effects can be accounted for with a multiconfigurational approach and outline the basic principles and performance. It is also shown how a detailed analysis of experimental spectra can be used to extract additional information about the electronic structure.
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| 34. |
- Manni, Giovanni Li, et al.
(författare)
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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.
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| 35. |
- Marazzi, Marco, et al.
(författare)
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Benzophenone Ultrafast Triplet Population : Revisiting the Kinetic Model by Surface-Hopping Dynamics
- 2016
-
Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 7:4, s. 622-626
-
Tidskriftsartikel (refereegranskat)abstract
- The photochemistry of benzophenone, a paradigmatic organic molecule for photosensitization, was investigated by means of surface-hopping ab initio molecular dynamics. Different mechanisms were found to be relevant within the first 600 fs after excitation; the long debated direct (S-1 -> T-1) and indirect (S-1 -> T-2 -> T-1) mechanisms for population of the low-lying triplet state are both possible, with the latter being prevalent. Moreover, we established the existence of a kinetic equilibrium between the two triplet states, never observed before. This fact implies that a significant fraction of the overall population resides in T-2, eventually allowing one to revisit the usual spectroscopic assignment proposed by transient absorption spectroscopy. This finding is of particular interest for photocatalysis as well as for DNA damages studies because both T-1 and T-2 channels are, in principle, available for benzophenone-mediated photoinduced energy transfer toward DNA.
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| 36. |
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| 37. |
- Pinjari, Rahul V., et al.
(författare)
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Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra
- 2016
-
Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 477-486
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Tidskriftsartikel (refereegranskat)abstract
- The restricted active-space (RAS) approach can accurately simulate metal L-edge X-ray absorption spectra of first-row transition metal complexes without the use of any fitting parameters. These characteristics provide a unique capability to identify unknown chemical species and to analyze their electronic structure. To find the best balance between cost and accuracy, the sensitivity of the simulated spectra with respect to the method variables has been tested for two models, [FeCl6](3-) and [Fe(CN)(6)](3-). For these systems, the reference calculations give deviations, when compared with experiment, of 1 eV in peak positions, 30% for the relative intensity of major peaks, and 50% for minor peaks. When compared with these deviations, the simulated spectra are sensitive to the number of final states, the inclusion of dynamical correlation, and the ionization potential electron affinity shift, in addition to the selection of the active space. The spectra are less sensitive to the quality of the basis set and even a double- basis gives reasonable results. The inclusion of dynamical correlation through second-order perturbation theory can be done efficiently using the state-specific formalism without correlating the core orbitals. Although these observations are not directly transferable to other systems, they can, together with a cost analysis, aid in the design of RAS models and help to extend the use of this powerful approach to a wider range of transition metal systems.
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| 38. |
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| 39. |
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| 40. |
- Pinjari, Rahul V., et al.
(författare)
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Restricted active space calculations of L-edge X-ray absorption spectra : From molecular orbitals to multiplet states
- 2014
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 141:12
-
Tidskriftsartikel (refereegranskat)abstract
- The metal L-edge (2p -> 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe3+, high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)(6)](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.
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| 41. |
- Roca-Sanjuán, Daniel, et al.
(författare)
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Chemiluminescence and Fluorescence States of a Small Model for Coelenteramide and Cypridina Oxyluciferin : A CASSCF/CASPT2 Study
- 2011
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 7:12, s. 4060-4069
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Tidskriftsartikel (refereegranskat)abstract
- Fluorescence and chemiluminescence phenomena are often confused in experimental and theoretical studies on the luminescent properties of chemical systems. To establish the patterns that distinguish both processes, the fluorescent and chemiluminescent states of 2-acetamido-3-methylpyrazine, which is a small model of the coelenterazine/coelenteramide and Cypridina luciferin/oxyluciferin bioluminescent systems, were characterized by using the complete active space second-order perturbation (CASPT2) method. Differences in geometries and electronic structures among the states responsible for light emission were found. On the basis of the findings, some recommendations for experimental studies on chemiluminescence are suggested, and more appropriate theoretical approaches are proposed.
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| 42. |
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| 43. |
- Rodrigues, Gabriel L. S., et al.
(författare)
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Multiconfigurational pair-density functional theory is more complex than you may think
- 2023
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:44, s. 9381-9388
-
Tidskriftsartikel (refereegranskat)abstract
- Multiconfigurational pair-density functional theory (MC-PDFT) is a promising way to describe both strong and dynamic correlations in an inexpensive way. The functionals in MC-PDFT are often “translated” from standard spin density functionals. However, these translated functionals can in principle lead to “translated spin densities” with a nonzero imaginary component. Current developments so far neglect this imaginary part by simply setting it to zero. In this work, we show how this imaginary component is actually needed to reproduce the correct physical behavior in a range of cases, especially low-spin open shells. We showcase the resulting formalism on both local density approximation and generalized gradient approximation functionals and illustrate the numerical behavior by benchmarking a number of singlet-triplet splittings (ST gaps) of organic diradicals and low-lying excited states of some common organic molecules. The results demonstrate that this scheme improves existing translated functionals and gives more accurate results, even with minimal active spaces.
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| 44. |
- Schnorr, Kirsten, et al.
(författare)
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Tracing the 267 nm-Induced Radical Formation in Dimethyl Disulfide Using Time-Resolved X-ray Absorption Spectroscopy
- 2019
-
Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 10:6, s. 1382-1387
-
Tidskriftsartikel (refereegranskat)abstract
- Disulfide bonds are pivotal for the structure, function, and stability of proteins, and understanding ultraviolet (UV)-induced S–S bond cleavage is highly relevant for elucidating the fundamental mechanisms underlying protein photochemistry. Here, the near-UV photodecomposition mechanisms in gas-phase dimethyl disulfide, a prototype system with a S–S bond, are probed by ultrafast transient X-ray absorption spectroscopy. The evolving electronic structure during and after the dissociation is simultaneously monitored at the sulfur L1,2,3-edges and the carbon K-edge with 100 fs (FWHM) temporal resolution using the broadband soft X-ray spectrum from a femtosecond high-order harmonics light source. Dissociation products are identified with the help of ADC and RASPT2 electronic-structure calculations. Rapid dissociation into two CH3S radicals within 120 ± 30 fs is identified as the major relaxation pathway after excitation with 267 nm radiation. Additionally, a 30 ± 10% contribution from asymmetric CH3S2 + CH3 dissociation is indicated by the appearance of CH3 radicals, which is, however, at least partly the result of multiphoton excitation.
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| 45. |
- Scott, Mikael, et al.
(författare)
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Complex Linear Response Functions for a Multiconfigurational Self-Consistent Field Wave Function in a High Performance Computing Environment
- 2023
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:17, s. 5924-5937
-
Tidskriftsartikel (refereegranskat)abstract
- We present novel developments for the highly efficient evaluation of complex linear response functions of a multiconfigurational self-consistent field (MCSCF) wave function as implemented in MultiPsi. Specifically, expressions for the direct evaluation of linear response properties at given frequencies using the complex polarization propagator (CPP) approach have been implemented, within both the Tamm-Dancoff approximation (TDA) and the random phase approximation (RPA). Purely real algebra with symmetric and antisymmetric trial vectors in a shared subspace is used wherein the linear response equations are solved. Two bottlenecks of large scale MC-CPP calculations, namely, the memory footprint and computational time, are addressed. The former is addressed by limiting the size of the subspace of trial vectors by using singular value decomposition (SVD) on either orbital or CI subspaces. The latter is addressed using an efficient parallel implementation as well as the strategy of dynamically adding linear response equations at near-convergence to neighboring roots. Furthermore, a novel methodology for decomposing MC-CPP spectra in terms of intuitive orbital excitations in an approximate fashion is presented. The performance of the code is illustrated with several numerical examples, including the X-ray spectrum of a molecule with nearly one hundred atoms. Additionally, for X-ray spectroscopy, the effect of including or excluding the core orbital in the active space on small covalent metal complexes is discussed.
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| 46. |
- Scott, Mikael, et al.
(författare)
-
Variational Pair-Density Functional Theory : Dealing with Strong Correlation at the Protein Scale
- 2024
-
Ingår i: Journal of Chemical Theory and Computation. - 1549-9618. ; 20:6
-
Tidskriftsartikel (refereegranskat)abstract
- Multiconfigurational pair-density functional theory (MC-PDFT) offers a promising solution to the challenges faced by traditional density functional theory (DFT) in addressing molecular systems containing transition metals, open-shells, or strong correlations in general. By utilizing both the density and on-top pair-density, MC-PDFT can make use of a more flexible multiconfigurational wave function to capture the necessary static correlation, while the pair-density functional also includes the effect of dynamic correlation. So far, MC-PDFT has been used after a multiconfigurational self-consistent field (MCSCF) step, using the orbitals and configuration interaction coefficients from the converged MCSCF wave function to compute PDFT energies and properties. Here, instead, we propose to perform a direct optimization of the wave function using the pair-density functionals, resulting in a variational formulation of MC-PDFT. We derive the expressions for the wave function gradient and illustrate their similarity to standard MCSCF equations. Furthermore, we illustrate the accuracy on a set of singlet-triplet gaps as well as dissociation curves. Our findings highlight one of MC-PDFT’s standout features: a reduced dependency on the active space size compared to conventional multiconfigurational wave function methodologies. Additionally, we show that the computational cost of MC-PDFT is potentially lower than MCSCF and often on-par with standard Kohn-Sham DFT, which is demonstrated by performing a MC-PDFT calculation of the entire ferredoxin protein with 1447 atoms and nearly 12 000 basis functions.
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| 47. |
- Vacher, Morgane, et al.
(författare)
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Origin of core-to-core x-ray emission spectroscopy sensitivity to structural dynamics
- 2020
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 7:4
-
Tidskriftsartikel (refereegranskat)abstract
- Recently, coherent structural dynamics in the excited state of an iron photosensitizer was observed through oscillations in the intensity of K alpha x-ray emission spectroscopy (XES). Understanding the origin of the unexpected sensitivity of core-to-core transitions to structural dynamics is important for further development of femtosecond time-resolved XES methods and, we believe, generally necessary for interpretation of XES signals from highly non-equilibrium structures that are ubiquitous in photophysics and photochemistry. Here, we use multiconfigurational wavefunction calculations combined with atomic theory to analyze the emission process in detail. The sensitivity of core-to-core transitions to structural dynamics is due to a shift of the minimum energy metal-ligand bond distance between 1s and 2p core-hole states. A key effect is the additional contraction of the non-bonding 3s and 3p orbitals in 1s core-hole states, which decreases electron-electron repulsion and increases overlap in the metal-ligand bonds. The effect is believed to be general and especially pronounced for systems with strong bonds. The important role of 3s and 3p orbitals is consistent with the analysis of radial charge and spin densities and can be connected to the negative chemical shift observed for many transition metal complexes. The XES sensitivity to structural dynamics can be optimized by tuning the emission energy spectrometer, with oscillations up to +/- 4% of the maximum intensity for the current system. The theoretical predictions can be used to design experiments that separate electronic and nuclear degrees of freedom in ultrafast excited state dynamics.
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| 48. |
- Vancoillie, Steven, et al.
(författare)
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Parallelization of a multiconfigurational perturbation theory
- 2013
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 34:22, s. 1937-1948
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we present a parallel approach to complete and restricted active space second-order perturbation theory, (CASPT2/RASPT2). We also make an assessment of the performance characteristics of its particular implementation in the Molcas quantum chemistry programming package. Parallel scaling is limited by memory and I/O bandwidth instead of available cores. Significant time savings for calculations on large and complex systems can be achieved by increasing the number of processes on a single machine, as long as memory bandwidth allows, or by using multiple nodes with a fast, low-latency interconnect. We found that parallel efficiency drops below 50% when using 8-16 cores on the shared-memory architecture, or 16-32 nodes on the distributed-memory architecture, depending on the calculation. This limits the scalability of the implementation to a moderate amount of processes. Nonetheless, calculations that took more than 3 days on a serial machine could be performed in less than 5 h on an InfiniBand cluster, where the individual nodes were not even capable of running the calculation because of memory and I/O requirements. This ensures the continuing study of larger molecular systems by means of CASPT2/RASPT2 through the use of the aggregated computational resources offered by distributed computing systems. (c) 2013 Wiley Periodicals, Inc.
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