| 1. |
- Abrikosov, Alexei I., et al.
(författare)
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Multiscale Modelling of Atomistic Structure of Calcium Silicate Hydrate
- 2022
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Ingår i: Solid State Phenomena. - Bäch, Switzerland : Scientific.Net. - 1012-0394 .- 1662-9779. ; 338, s. 123-128
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Tidskriftsartikel (refereegranskat)abstract
- The atomistic structure of calcium-silicate-hydrate (C-S-H) has been studied by applying force field simulations and quantum mechanical methods. Large number of crystallographically equivalent structures were used to account for the disordered nature of C-S-H. An extensive set of periodic structures of C-S-H (with a variation of chemical composition) has been generated and optimised. Special attention has been paid to two crystallographic models for tobermorite, which are used for the construction of C-S-H models. Re-optimisation of atomic structures, initially optimised with ReaxFF force field, by quantum chemical methods (semiempirical and Density functional theory) have been performed. Although the main structural characteristics of C-S-H remain the same in all calculations, the balance between the amount of OH groups and water in the structure is different. The obtained structures (optimised with a different level of theory) are combined into an on-line database and can be used for a future simulation of C-S-H materials.
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| 2. |
- Abrikosov, Alexei I., et al.
(författare)
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Multiscale study of crystal and electronic structure of Al defects in concrete
- 2018
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Ingår i: International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018. - : Author(s). - 9780735417663 ; 2040
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Konferensbidrag (refereegranskat)abstract
- Possible crystal structures of aluminium defects in concrete materials are tested with reactive force filed ReaxFF. The ongoing project includes further refinement of the structures by semiempirical and ab initio methods.
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| 3. |
- 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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| 4. |
- Aquilante, Francesco, et al.
(författare)
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Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table
- 2016
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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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| 5. |
- Aquilante, Francesco, et al.
(författare)
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MOLCAS-a software for multiconfigurational quantum chemistry calculations
- 2013
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0884 .- 1759-0876. ; 3:2, s. 143-149
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Tidskriftsartikel (refereegranskat)abstract
- At variance, with most of the quantum chemistry software presently available, MOLCAS is a package that is specialized in multiconfigurational wave function theory (MC-WFT) rather than density functional theory (DFT). Given the much higher algorithmic complexity of MC-WFT versus DFT, an extraordinary effort needs to be made from the programming point of view to achieve state-of-the-art performance for large-scale calculations. In particular, a robust and efficient implementation of the Cholesky decomposition techniques for handling two-electron integrals has been developed which is unique to MOLCAS. Together with this 'Cholesky infrastructure', a powerful and multilayer graphical and scripting user interface is available, which is an essential ingredient for the setup of MC-WFT calculations. These two aspects of the MOLCAS software constitute the focus of the present report. (C) 2012 John Wiley & Sons, Ltd.
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| 6. |
- Aquilante, Francesco, et al.
(författare)
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Software news and update MOLCAS 7 : The Next Generation
- 2010
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 31:1, s. 224-247
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Forskningsöversikt (refereegranskat)abstract
- Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.
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| 7. |
- Azizi, Zahra, et al.
(författare)
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How accurate is the CASPT2 method?
- 2006
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 8:23, s. 2727-2732
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Tidskriftsartikel (refereegranskat)abstract
- This paper is a reply to a recent paper on the isomers of trisulfur oxides (Chem. Commun., 2005, 3712) where the accuracy of the CASPT2 method is called in question. We illustrate that their results are due to an inadequate choice of active orbitals. Some results for related O and S containing molecules are also presented to strengthen the argumentation. It is concluded that the CASPT2 method is accurate to at least 0.1 eV (2 kcal mol(-1)) for this type of systems.
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| 8. |
- Bolaño, Iria, et al.
(författare)
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Pyridine-cyanoanthracene bonded exciplex
- 2019
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Ingår i: Proceedings of the International Conference of Computational Methods in Sciences and Engineering 2019, ICCMSE 2019. - : AIP Publishing. - 0094-243X .- 1551-7616. - 9780735419339 ; 2186
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Konferensbidrag (refereegranskat)abstract
- Exiplexes are a special kind of molecular complexes, which exist only due to a weak bond in an excited state. The theoretical description of these complexes requires the usage of multiconfigurational theory (CASSCF or RASSCF) followed by second order of perturbation theory. Formation of exiplex complex from pyridine and cyano-anthracene has been studied.
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| 9. |
- Boström, Jonas, et al.
(författare)
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Analytical gradients of the second-order Møller–Plesset energy using Cholesky decompositions
- 2014
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 114:5, s. 321-327
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Tidskriftsartikel (refereegranskat)abstract
- An algorithm for computing analytical gradients of the second-order Møller–Plesset (MP2) energy using density fitting (DF) is presented. The algorithm assumes that the underlying canonical Hartree–Fock reference is obtained with the same auxiliary basis set, which we obtain by Cholesky decomposition (CD) of atomic electron repulsion integrals. CD is also used for the negative semidefinite MP2 amplitude matrix. Test calculations on the weakly interacting dimers of the S22 test set (Jurečka et al., Phys. Chem. Chem. Phys. 2006, 8, 1985) show that the geometry errors due to the auxiliary basis set are negligible. With double-zeta basis sets, the error due to the DF approximation in intermolecular bond lengths is better than 0.1 pm. The computational time is typically reduced by a factor of 6–7.
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| 10. |
- Bywater, Robert P, et al.
(författare)
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The dipeptide conformations of all twenty amino acid types in the context of biosynthesis.
- 2015
-
Ingår i: SpringerPlus. - : Springer Science and Business Media LLC. - 2193-1801. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- There have been many studies of dipeptide structure at a high level of accuracy using quantum chemical methods. Such calculations are resource-consuming (in terms of memory, CPU and other computational imperatives) which is the reason why most previous studies were restricted to the two simplest amino-acid residue types, glycine and alanine. We improve on this by extending the scope of residue types to include all 20 naturally occurring residue types. Our results reveal differences in secondary structure preferences for the all residue types. There are in most cases very deep energy troughs corresponding either to the polyproline II (collagen) helix and the α-helix or both. The β-strand was not strongly favoured energetically although the extent of this depression in the energy surface is, while not "deeper" (energetically), has a wider extent than the other two types of secondary structure. There is currently great interest in the question of cotranslational folding, the extent to which the nascent polypeptide begins to fold prior to emerging from the ribosome exit tunnel. Accordingly, while most previous quantum studies of dipeptides were carried out in the (simulated) gas or aqueous phase, we wished to consider the first step in polypeptide biosynthesis on the ribosome where neither gas nor aqueous conditions apply. We used a dielectric constant that would be compatible with the water-poor macromolecular (ribosome) environment.
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| 11. |
- Bywater, Robert P., et al.
(författare)
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The preferred conformation of dipeptides in the context of biosynthesis
- 2013
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Ingår i: Naturwissenschaften. - : Springer Science and Business Media LLC. - 1432-1904 .- 0028-1042. ; 100:9, s. 853-859
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Tidskriftsartikel (refereegranskat)abstract
- Globular proteins are folded polypeptide structures comprising stretches of secondary structures (helical (alpha- or 3(10) helix type), polyproline helix or beta-strands) interspersed by regions of less well-ordered structure ("random coil"). Protein fold prediction is a very active field impacting inte alia on protein engineering and misfolding studies. Apart from the many studies of protein refolding from the denatured state, there has been considerable interest in studying the initial formation of peptides during biosynthesis, when there are at the outset only a few residues in the emerging polypeptide. Although there have been many studies employing quantum chemical methods of the conformation of dipeptides, these have mostly been carried out in the gas phase or simulated water. None of these conditions really apply in the interior confines of the ribosome. In the present work, we are concerned with the conformation of dipeptides in this low dielectric environment. Furthermore, only the residue types glycine and alanine have been studied by previous authors, but we extend this repertoire to include leucine and isoleucine, position isomers which have very different structural propensities.
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| 12. |
- de Jong, Wibe A, et al.
(författare)
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Utilizing high performance computing for chemistry : parallel computational chemistry
- 2010
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 12:26, s. 6896-6920
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Tidskriftsartikel (refereegranskat)abstract
- Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.
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| 13. |
- 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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| 14. |
- Johansson, Marcus, et al.
(författare)
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Automatic procedure for generating symmetry adapted wavefunctions
- 2017
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Ingår i: Journal of Cheminformatics. - : Springer Science and Business Media LLC. - 1758-2946. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an implementation are presented. The symmetry detection algorithm is a clustering algorithm for symmetry invariant properties, combined with logical deduction of possible symmetry elements using the geometry of sets of symmetrically equivalent atoms. An algorithm for determining the symmetry adapted linear combinations (SALCs) of atomic orbitals is also presented. The SALCs are constructed with the use of projection operators for the irreducible representations, as well as subgroups for determining splitting fields for a canonical basis. The character tables for the point groups are auto generated, and the algorithm is described. Symmetrisation of molecules use a projection into the totally symmetric space, whereas for wavefunctions projection as well and partner function determination and averaging is used. The software has been released as a stand-alone, open source library under the MIT license and integrated into both computational and molecular modelling software. Graphical abstract.
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| 15. |
- Karlström, Gunnar, et al.
(författare)
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MOLCAS : a program package for computational chemistry
- 2003
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Ingår i: Computational materials science. - 0927-0256 .- 1879-0801. ; 28:2, s. 222-239
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Tidskriftsartikel (refereegranskat)abstract
- The program system MOLCAS is a package for calculations of electronic and structural properties of molecular systems in gas, liquid, or solid phase. It contains a number of modern quantum chemical methods for studies of the electronic structure in ground and excited electronic states. A macromolecular environment can be modeled by a combination of quantum chemistry and molecular mechanics. It is further possible to describe a crystalline material using model potentials. Solvent effects can be treated using continuum models or by combining quantum chemical calculations with molecular dynamics or Monte-Carlo simulations. MOLCAS is especially adapted to treat systems with a complex electronic structure, where the simplest quantum chemical models do not work. These features together with the inclusion of relativistic effects makes it possible to treat with good accuracy systems including atoms from the entire periodic system. MOLCAS has effective methods for geometry optimization of equilibria, transition states, conical intersections, etc. This facilitates studies of excited state energy surfaces, spectroscopy, and photochemical processes.
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| 16. |
- Kocherbitov, Vitaly, et al.
(författare)
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Hydration of trimethylamine-N-oxide and of dimethyldodecylamine-N-oxide: An ab initio study
- 2007
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Ingår i: Journal of molecular structure. Theochem. - : Elsevier BV. - 0166-1280. ; 808:1-3, s. 111-118
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Tidskriftsartikel (refereegranskat)abstract
- Density functional theory (B3LYP) calculations of the hydration of trimethylamine-N-oxide (TMAO) and a surfactant dimethyldodecylamine-N-oxide (DDAO) are reported. Hydrogen-bonded complexes of DDAO with up to three water molecules and of TMAO with up to five water molecules are studied. Interactions of both TMAO and DDAO with water give rise to the binding energies that are much higher than that in the water dimer. A significant charge transfer from amine oxide to water is observed. Energies of water-water interactions increase in the presence of amine oxides. The hydration number of TMAO in the hydrogen bonded complexes is shown to be three. The energies of amine oxide-water interactions in the hydrogen bonded complexes have been analyzed using differential energetic parameters analogous to the parameters measured in calorimetric experiments.
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| 17. |
- Kocherbitov, Vitaly, et al.
(författare)
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Hydrogen bonding in glassy trehalose-water system : Insights from density functional theory and molecular dynamics simulations
- 2024
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 160:8
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Tidskriftsartikel (refereegranskat)abstract
- We report a detailed density functional theory and molecular dynamics study of hydrogen bonding between trehalose and water, with a special emphasis on interactions in the amorphous solid state. For comparison, water-water interactions in water dimers and tetramers are evaluated using quantum calculations. The results show that the hydrogen bonding energy is dependent not only on the geometry (bond length and angle) but also on the local environment of the hydrogen bond. This is seen in quantum calculations of complexes in vacuum as well as in amorphous solid states with periodic boundary conditions. The temperature-induced glass transition in the trehalose-water system was studied using molecular dynamics simulations with varying cooling and heating rates. The obtained parameters of the glass transition are in good agreement with the experiments. Moreover, the dehydration of trehalose in the glassy state was investigated through a gradual dehydration with multiple small steps under isothermal conditions. From these simulations, the values of water sorption energy at different temperatures were obtained. The partial molar enthalpy of mixing of water value of −18 kJ/mol found in calorimetric experiments was accurately reproduced in these simulations. These findings are discussed in light of the hydrogen bonding data in the system. We conclude that the observed exothermic effect is due to different responses of liquid and glassy matrices to perturbations associated with the addition or removal of water molecules.
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| 18. |
- Kovacevic, Goran, et al.
(författare)
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Atomistic modeling of crystal structure of Ca1.67SiHx
- 2015
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Ingår i: Cement and Concrete Research. - : Elsevier BV. - 0008-8846. ; 67, s. 197-203
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Tidskriftsartikel (refereegranskat)abstract
- The atomic structure of calcium-silicate-hydrate (C-1.67-S-H-x) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three models. The C-S-H model related to the lowest energy is considered as the most probable. It turns out to be characterized by the distribution of dimeric and pentameric silicates and the absence of monomers. This model has mass density which is closest to the experimental one. (C) 2014 Elsevier Ltd. All rights reserved.
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| 19. |
- Kovačević, Goran, et al.
(författare)
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Luscus: molecular viewer and editor for MOLCAS.
- 2015
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Ingår i: Journal of Cheminformatics. - : Springer Science and Business Media LLC. - 1758-2946. ; 7, s. 16-16
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Tidskriftsartikel (refereegranskat)abstract
- The novel program for graphical display and editing of molecular systems, luscus, is described. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling. Graphical AbstractScreenshot of luscus program showing molecular orbital.
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| 20. |
- Kovačević, Goran, et al.
(författare)
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Revised atomistic models of the crystal structure of C-S-H with high C/S ratio
- 2016
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Ingår i: Zeitschrift fur Physikalische Chemie. - : Walter de Gruyter GmbH. - 0942-9352 .- 2196-7156. ; 230:9, s. 1411-1424
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Tidskriftsartikel (refereegranskat)abstract
- The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been studied. Atomistic C-S-H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the diferent structures. An extensive set of periodic structures of C-S-H with variation of water content was created, and then optimized using molecular dynamics with reactive force feld ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C-S-H. The new geometries of C-S-H, reported in this paper, show lower relative energy with respect to the geometries from the original defnition of C-S-H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values.
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| 21. |
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| 22. |
- La Macchia, Giovanni, et al.
(författare)
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Bond Length and Bond Order in One of the Shortest Cr-Cr Bonds
- 2008
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 47:24, s. 11455-11457
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Tidskriftsartikel (refereegranskat)abstract
- Multiconfigurational quantum chemical calculations on the R-diimines dichromium compound confirm that the Cr-Cr bond, 1.80 angstrom, is among the shortest Cr-I-Cr-I bonds. However, the bond between the two Cr atoms is only a quadruple bond rather than a quintuple bond. The reason why the bond is so short has to be attributed to the strain in the NCCN ligand moieties.
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| 23. |
- Larsson, Dennis, et al.
(författare)
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An embedded cluster CASPT2 study of the Ce:YVO4 spectrum
- 2023
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Ingår i: The Journal of chemical physics. - 0021-9606. ; 159:11
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Tidskriftsartikel (refereegranskat)abstract
- Multiconfigurational theory, in combination with the embedded cluster approach, is a precise and ab initio approach to describe the electronic structure of solids. In this work, the spectrum of a Ce(III) dopant in YVO4 has been studied by complete active space perturbation theory of the second order (CASPT2), with the host material represented as a set of ab initio model potentials and point-charges. We assess the sensitivity of the spectrum to the size of both the embedded cluster size as well as the size of the electronic basis set. A comparison of our best computational model with experimental results shows that the embedding approach is robust and can accurately model the spectrum of low-concentration dopants in complex host materials.
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| 24. |
- Larsson, Ernst D., et al.
(författare)
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A program system for self-consistent embedded potentials for ionic crystals
- 2022
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Ingår i: Chemical Physics. - : Elsevier BV. - 0301-0104. ; 562
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Tidskriftsartikel (refereegranskat)abstract
- Embedded-cluster models of crystalline solids are important to allow accurate wave function methods to be applicable to solids. The ab initio model potential method for embedding ionic solids has historically been shown to be a viable tool. While useful, the method has been limited by the need to generate such potentials for each crystal structure and the lack of a freely available program for generating ab initio model potentials. Herein, this is remedied by showcasing a new, AFL licensed, program, SCEPIC, which can be used in combination with Molcas or OpenMolcas codes to derive ab initio model potentials for ionic crystals. The applicability of ab initio model potentials derived via SCEPIC is evaluated for three simple ionic solids: MgO, CaO and CaF2. The following questions are addressed: (i) the capability of the method to reproduce the density matrix from periodic density functional theory calculations, (ii) the feasibility of performing geometry optimisations, (iii) the possibility to model band gaps of insulators and (iv) the ligand-field splitting of Ni-doped MgO. Going beyond the classical restriction of parametrising ab initio model potentials only at the Hartree–Fock level-of-theory, this work additionally address the sensitivity of results to the underlying Hamiltonian used to derive the potentials. The results demonstrate that good agreement with periodic density functional theory calculations can be achieved, geometry optimisations are feasible and accurate band gaps and ligand-field splittings can be computed.
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| 25. |
- Larsson, Ernst D., et al.
(författare)
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Convergence of Electronic Structure Properties in Ionic Oxides Within a Fragment Approach
- 2022
-
Ingår i: Frontiers in Chemistry. - : Frontiers Media SA. - 2296-2646. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Embedded-cluster models of crystalline solids are important to allow accurate wave function methods to be applicable to solids. The ab-initio model potential method, in which the crystal is divided into three different fragments, one quantum fragment, one ab-initio model potential fragment and one point-charge fragment, has historically been shown to be a viable tool for describing the electronic structure in ionic solids. The optimal size of these regions is, of course, individual for each crystal. In this study we analyzed the convergence of the electronic structure properties with respect to an increase of the size of the quantum part and the layer of potentials. MgO crystal and Ni: MgO were used for this purpose as examples of an ideal crystal and a crystal with a point defect. We demonstrated that with an increase of the cluster size, the electron density in the inner part of the cluster becomes very similar to the electron density in the periodic model. Clusters, embedded into a layer of model potential and electrostatic field, are a good alternative to periodic description.
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| 26. |
- Larsson, Ernst D., et al.
(författare)
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Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes
- 2020
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 49:5, s. 1501-1512
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Tidskriftsartikel (refereegranskat)abstract
- The lytic polysaccharide monooxygenase (LPMO) enzymes boost polysaccharide depolymerization through oxidative chemistry, which has fueled the hope for more energy-efficient production of biofuel. We have recently proposed a mechanism for the oxidation of the polysaccharide substrate (E. D. Hedegård and U. Ryde, Chem. Sci., 2018, 9, 3866-3880). In this mechanism, intermediates with superoxide, oxyl, as well as hydroxyl (i.e. [CuO2]+, [CuO]+ and [CuOH]2+) cores were involved. These complexes can have both singlet and triplet spin states, and both spin-states may be important for how LPMOs function during catalytic turnover. Previous calculations on LPMOs have exclusively been based on density functional theory (DFT). However, different DFT functionals are known to display large differences for spin-state splittings in transition-metal complexes, and this has also been an issue for LPMOs. In this paper, we study the accuracy of DFT for spin-state splittings in superoxide, oxyl, and hydroxyl intermediates involved in LPMO turnover. As reference we employ multiconfigurational perturbation theory (CASPT2).
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| 27. |
- Malmqvist, Per-Åke, et al.
(författare)
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The binatural orbitals of electronic transitions
- 2012
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Ingår i: Molecular Physics. - : Informa UK Limited. - 1362-3028 .- 0026-8976. ; 110:19-20, s. 2455-2464
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Tidskriftsartikel (refereegranskat)abstract
- The well-known natural orbitals are defined as eigenfunctions of a one-particle reduced density operator, and can be obtained from a computed density matrix by diagonalization. Similarly, in this article we define the binatural orbitals, which are obtained for a pair of wave functions by a singular value decomposition of a reduced transition density matrix. The pair of states would usually be eigenstates of the electronic Hamiltonian, and the binatural orbitals then serve as a useful tool for the analysis of the transition between these states. More generally, application to any two state functions gives important information as to how the two states differ. Some examples are shown.
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| 28. |
- 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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| 29. |
- Masso, H., et al.
(författare)
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Ab initio characterization of C-5
- 2007
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 127:15
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, the structure and spectroscopic parameters of the C-5 cluster are determined using multiconfigurational quantum chemical methods as implemented in the MOLCAS software. A number of spectroscopic properties (band center positions, l-doubling parameters, and rotational constants) have been characterized. From the new results, the assignments of previous astrophysical observations [J. Goicoechea , Astrophys. J. 609, 225 (2004)] are discussed. A detailed exploration of the global potential energy surface confirms that C-5 has a X (1)Sigma(+)(g) linear isomer of prominent stability and, at least, three minimum energy structures showing singlet electronic ground states. Two of them are cyclic and one has a nonplanar geometry. Vertical and adiabatic electronic transitions and vibrational spectroscopic parameters are determined for the most stable linear isomer using multiconfigurational second order perturbation theory (CASPT2) using an active space containing 12 valence orbitals with 12 active electrons and extended ANO-type basis sets. The infrared spectrum has been analyzed from an anharmonic force field derived form the local surface, determined from the energies of a grid of 1350 geometries. The force field includes four coupling terms. The CASPT2 band center position of the nu(7)(pi(u)) anharmonic fundamental has been calculated to be at 102 cm(-1), which validates the assignment to C-5 of the pattern of bands centered at 102 cm(-1) observed with the ISO telescope. (C) 2007 American Institute of Physics.
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| 30. |
- Naderi, Fereshteh, et al.
(författare)
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Multiconfigurational Study of the Electronic Structure of Negatively Charged Fullerens
- 2017
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Ingår i: Journal of Chemistry and Chemical Engineering. - : David Publishing Company. - 1934-7375 .- 1934-7383. ; 11, s. 30-30
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Tidskriftsartikel (refereegranskat)abstract
- Multiconfigurational second order perturbation theory was employed in order to describe the ground and excited states of C_60^(-n). Different choices of the active spaces are discussed and the possibility to apply multiconfigurational theory to study C_120 is investigated. The calculations were performed for all possible spin states (for selected charge) and show the preference of low spin state. The energy difference between two C_60^(-3) and pairs C_60^(-1)- C_60^(-5) and C_60^(-2)- C_60^(-4) shows that the probability to create a charge alternation in fullerides is small.
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| 31. |
- Naderi, Fereshteh, et al.
(författare)
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The electronic structure of negatively charged fullerenes : From monomers to dimers
- 2017
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Ingår i: Proceedings of the International Conference of Computational Methods in Sciences and Engineering 2017, ICCMSE 2017. - : Author(s). - 9780735415966 ; 1906
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Konferensbidrag (refereegranskat)abstract
- Multiconfigurational second order perturbation theory was employed in order to describe the ground and excited states of negatively charged fullerenes C60 and fullerene dimers C120. The calculations were performed for all possible spin states. The obtained results can be used to understand the electronic structure of fullerides.
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| 32. |
- Rocha-Rinza, Tomas, et al.
(författare)
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A theoretical study of singlet low-energy excited states of the benzene dimer
- 2006
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 426:4-6, s. 268-272
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Tidskriftsartikel (refereegranskat)abstract
- The singlet ground and low-energy excited states of the benzene dimer in D-6h geometry are characterized using second order multireference perturbation theory (CASPT2). The counterpoise-corrected spectroscopic parameters of the benzene excimer are in quantitative agreement with experiment. The same method was used to compute a submanifold of the potential energy hypersurface of the first excited state of the benzene dimer, exhibiting two local minima in addition to a saddle point between them. This study demonstrates the suitability of CASPT2 to describe the benzene excimer and suggests that the method can be used to describe weak intermolecular interactions involving excited states. (c) 2006 Elsevier B.V. All rights reserved.
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| 33. |
- Roos, Björn, et al.
(författare)
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Main group atoms and dimers studied with a new relativistic ANO basis set
- 2004
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 108:15, s. 2851-2858
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Tidskriftsartikel (refereegranskat)abstract
- New basis sets of the atomic natural orbital (ANO) type have been developed for the main group and rare gas atoms. The ANO’s have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive and negative ions, and the dimer at its equilibrium geometry. Scalar relativistic effects are included through the use of a Douglas-Kroll Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies, electron affinities, and excitation energies for all atoms and the ground-state potentials for the dimers. These calculations include spin-orbit coupling using the RASSCF State Interaction (RASSI-SO) method. The spin-orbit splitting for the lowest atomic term is reproduced with an accuracy of better than 0.05 eV, except for row 5, where it is 0.15 eV. Ionization energies and electron affinities have an accuracy better than 0.2 eV, and atomic polarizabilities for the spherical atoms are computed with errors smaller than 2.5%. Computed bond energies for the dimers are accurate to better than 0.15 eV in most cases (the dimers for row 5 excluded).
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| 34. |
- Roos, Björn, et al.
(författare)
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New relativistic ANO basis sets for actinide atoms
- 2005
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 409:4-6, s. 295-299
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Tidskriftsartikel (refereegranskat)abstract
- New basis sets of the atomic natural orbital (ANO) type have been developed for the actinide atoms Ac-Cm. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive ions, and the atom in a electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies and some excitation energies. Computed ionization energies have an accuracy better than 0.2 eV in most cases. The lowest multiplet levels have been computed. These calculations include spin-orbit coupling using a variation-perturbation approach. The atomic polarizability of the spherically symmetric americium atom has been computed to be 116 au(3).
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| 35. |
- Roos, Björn, et al.
(författare)
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New relativistic ANO basis sets for transition metal atoms
- 2005
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 109:29, s. 6575-6579
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Tidskriftsartikel (refereegranskat)abstract
- New basis sets of the atomic natural orbital (ANO) type have been developed for the first, second, and third row transition metal atoms. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive and negative ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies, electron affinities, and excitation energies for all atoms and polarizabilities for spherically symmetric atoms. These calculations include spin-orbit coupling using a variation-perturbation approach. Computed ionization energies have an accuracy better than 0.2 eV in most cases. The accuracy of computed electron affinities is the same except in cases where the experimental values are smaller than 0.5 eV. Accurate results are obtained for the polarizabilities of atoms with spherical symmetry. Multiplet levels are presented for some of the third row transition metals.
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| 36. |
- Roos, Björn, et al.
(författare)
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New Relativistic Atomic Natural Orbital Basis Sets for Lanthanide Atoms with Applications to the Ce Diatom and LuF3
- 2008
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 112:45, s. 11431-11435
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Tidskriftsartikel (refereegranskat)abstract
- New basis sets of the atomic natural orbital (ANO) type have been developed for the lanthanide atoms La-Lu. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies and some excitation energies. Computed ionization energies have an accuracy better than 0.1 eV in most cases. Two molecular applications are inluded as illustration: the cerium diatom and the LuF3 molecule. In both cases it is shown that 4f orbitals are not involved in the chemical bond in contrast to an earlier claim for the latter molecule.
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| 37. |
- Roos, Björn, et al.
(författare)
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Not Innocent: Verdict from Ab Initio Multiconfigurational Second-Order Perturbation Theory on the Electronic Structure of Chloroiron Corrole
- 2008
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:45, s. 14099-14102
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Tidskriftsartikel (refereegranskat)abstract
- From a suitably broad perspective, transition metal corroles may be viewed as stable, synthetic analogues of high-valent heme protein intermediates such as compounds I and II. Against this backdrop, the electronic structure of chloroiron corrole has provoked a lively debate in recent years. Thus, whereas NMR spectroscopy and DFT calculations suggest an S = 3/2 Fe(III) corrole(center dot 2-) radical description, certain researchers have favored an Fe(IV) formulation. These two descriptions are indistinguishable as far as DFT calculations are concerned. Ab initio CASSCF/CASPT2 calculations provide unambiguous support for the former description. In addition, they rule out any Fe(IV) state, whether high- or low-spin, within 1.5 eV of the ground state.
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| 38. |
- Roos, Björn O., et al.
(författare)
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Multiconfigurational Quantum Chemistry
- 2016
-
Bok (refereegranskat)abstract
- The first book to aid in the understanding of multiconfigurational quantum chemistry, Multiconfigurational Quantum Chemistry demystifies a subject that has historically been considered difficult to learn. Accessible to any reader with a background in quantum mechanics and quantum chemistry, the book contains illustrative examples showing how these methods can be used in various areas of chemistry, such as chemical reactions in ground and excited states, transition metal and other heavy element systems. The authors detail the drawbacks and limitations of DFT and coupled-cluster based methods and offer alternative, wavefunction-based methods more suitable for smaller molecules.
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| 39. |
- Roos, Björn, et al.
(författare)
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Relativistic atomic natural orbital type basis sets for the alkaline and alkaline-earth atoms applied to the ground-state potentials for the corresponding dimers
- 2004
-
Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 111:2-6, s. 345-351
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Tidskriftsartikel (refereegranskat)abstract
- New basis sets of the atomic natural orbital (ANO) type have been developed for the atoms Li-Fr and Be-Ra. The ANOs have been obtained from the average density matrix of the ground states and the lowest excited states of the atom, the positive ion, and the dimer at its equilibirium geometry. Scalar realtivisitc effects are included through the use of a Douglas-Kroll Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of the ground-state potentials for the dimers. Computed bond energies are accurate to within 0.05 eV for the alkaline dimers and 0.02 eV for the alkaline-earth dimers (except for Be-2).
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| 40. |
- Schapiro, Igor, et al.
(författare)
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Synthesis, spectroscopy and QM/MM simulations of a biomimetic ultrafast light-driven molecular motor
- 2019
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Ingår i: Photochemical and Photobiological Sciences. - : Springer Science and Business Media LLC. - 1474-9092 .- 1474-905X. ; 18:9, s. 2259-2269
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Tidskriftsartikel (refereegranskat)abstract
- A molecular motor potentially performing a continuous unidirectional rotation is studied by a multidisciplinary approach including organic synthesis, transient spectroscopy and excited state trajectory calculations. A stereogenic center was introduced in the N-alkylated indanylidene-pyrroline Schiff base framework of a previously investigated light-driven molecular switch in order to achieve the unidirectional C[double bond, length as m-dash]C rotary motion typical of Feringa's motor. Here we report that the specific substitution pattern of the designed chiral molecule must critically determine the unidirectional efficiency of the light-induced rotary motion. More specifically, we find that a stereogenic center containing a methyl group and a hydrogen atom as substituents does not create a differential steric effect large enough to fully direct the motion in either the clockwise or counterclockwise direction especially along the E→Z coordinate. However, due to the documented ultrafast character and electronic circular dichroism activity of the investigated system, we find that it provides the basis for development of a novel generation of rotary motors with a biomimetic framework and operating on a picosecond time scale.
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| 41. |
- 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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| 42. |
- Vancoillie, Steven, et al.
(författare)
-
Potential Energy Surface of the Chromium Dimer Re-re-revisited with Multiconfigurational Perturbation Theory
- 2016
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 12:4, s. 1647-1655
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Tidskriftsartikel (refereegranskat)abstract
- The chromium dimer has long been a benchmark molecule to evaluate the performance of different computational methods ranging from density functional theory to wave function methods. Among the latter, multiconfigurational perturbation theory was shown to be able to reproduce the potential energy surface of the chromium dimer accurately. However, for modest active space sizes, it was later shown that different definitions of the zeroth-order Hamiltonian have a large impact on the results. In this work, we revisit the system for the third time with multiconfigurational perturbation theory, now in order to increase the active space of the reference wave function. This reduces the impact of the choice of zeroth-order Hamiltonian and improves the shape of the potential energy surface significantly. We conclude by comparing our results of the dissocation energy and vibrational spectrum to those obtained from several highly accurate multiconfigurational methods and experiment. For a meaningful comparison, we used the extrapolation to the complete basis set for all methods involved.
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| 43. |
- Veryazov, Valera, et al.
(författare)
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How to Select Active Space for Multiconfigurational Quantum Chemistry?
- 2011
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608. ; 111:13, s. 3329-3338
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Tidskriftsartikel (refereegranskat)abstract
- Bjorn Roos is one of the pioneers in the development and usage of multiconfigurational methods, in particular, the complete active space self-consistent field method and the perturbational complete active space perturbation theory through second order. To perform multiconfigurational calculations using these methods, a set of active orbitals must be selected, and the success of the methods depends on the choice of this set. This is not only sometimes easy but also sometimes difficult, especially for use of the more recent RASSCF and RASPT2 methods (which use a "restricted active space" rather than the complete one). Although an automated procedure for selecting the active orbitals would be a preferable solution, this does not seem feasible yet. An account of the problem is given, with examples and some approaches that usually work. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111: 3329-3338, 2011
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| 44. |
- Veryazov, Valera, et al.
(författare)
-
MOLCAS as a development platform for quantum chemistry software
- 2004
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 100:4, s. 626-635
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Tidskriftsartikel (refereegranskat)abstract
- This work presents the quantum chemistry package MOLCAS, with emphasis on its usefulness as a platform for developing new quantum chemical codes, and the reader is assumed to be familiar with such a process. The development of new codes for quantum chemistry is a time-consuming job that can be dramatically simplified by using libraries for standard problems (such as calculation of integrals), and tools to surmount computer language and operating system limitations. The MOLCAS quantum chemistry software contains modules for a variety of quantum chemical methods, such as Hartree-Fock (HF), density functional theory (DFT), coupled-cluster (CC), and multiconfigurational (MCSCF) approaches, including second-order perturbation theory. It runs on almost all UNIX-like platforms and contains a single source code for 32- and 64-bit architecture, as well as for serial and parallel execution. The MOLCAS environment allows the user to include, in a simple way, new codes integrated with libraries and other MOLCAS modules. The key features of the MOLCAS environment include a modular structure, an easy-to-use environment, an application programming interface (API) library for solving common computational and system-oriented problems, a solid verification control system, and tools for a distributed development.
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| 45. |
- Vysotskiy, Victor, et al.
(författare)
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A new module for constrained multi-fragment geometry optimization in internal coordinates implemented in the MOLCAS package.
- 2013
-
Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 34:30, s. 2657-2665
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Tidskriftsartikel (refereegranskat)abstract
- A parallel procedure for an effective optimization of relative position and orientation between two or more fragments has been implemented in the MOLCAS program package. By design, the procedure does not perturb the electronic structure of a system under the study. The original composite system is divided into frozen fragments and internal coordinates linking those fragments are the only optimized parameters. The procedure is capable to handle fully independent (no border atoms) fragments as well as fragments connected by covalent bonds. In the framework of the procedure, the optimization of relative position and orientation of the fragments are carried out in the internal "Z-matrix" coordinates using numerical derivatives. The total number of required single points energy evaluations scales with the number of fragments rather than with the total number of atoms in the system. The accuracy and the performance of the procedure have been studied by test calculations for a representative set of two- and three-fragment molecules with artificially distorted structures. The developed approach exhibits robust and smooth convergence to the reference optimal structures. As only a few internal coordinates are varied during the procedure, the proposed constrained fragment geometry optimization can be afforded even for high level ab initio methods like CCSD(T) and CASPT2. This capability has been demonstrated by applying the method to two larger cases, CCSD(T) and CASPT2 calculations on a positively charged benzene lithium complex and on the oxygen molecule interacting to iron porphyrin molecule, respectively. © 2013 Wiley Periodicals, Inc.
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| 46. |
- Wang, Xuefeng, et al.
(författare)
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A combined theoretical and experimental study of simple terminal group 6 nitride and phosphide N MX3 and P MX3 molecules
- 2008
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 112:35, s. 8030-8037
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Tidskriftsartikel (refereegranskat)abstract
- Organometallic complexes containing terminal metal nitrides and phosphides are important synthetic reagents. Laser-ablated group 6 metal atoms react with NF3, PF3, and PCl3 to form the simple lowest energy N MF3, and P MX3 products following insertion and halogen transfer, with the exception of P CrF3, which is a higher energy species and is not observed. The E MX3 pnictide metal trihalide molecules are identified from both argon and neon matrix infrared spectra and frequencies calculated by density functional theory and multiconfigurational second-order perturbation theory (CASSCF/CASPT2). These simple terminal nitrides involve strong triple bonds, which range from 2.80 to 2.77 to 2.59 natural bond order for M = W, Mo, and Cr, respectively, as computed by CASSCF/CASPT2, and the M N stretching frequencies also follow this order. The terminal phosphides are weaker with bond orders 2.74, 2.67, and 2.18, respectively, as the more diffuse 3p orbitals are less effective for bonding to the more compact metal valence d orbitals.
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| 47. |
- Wei, Yao, et al.
(författare)
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A comprehensive exploration of structural and electronic properties of molybdenum clusters
- 2024
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Ingår i: APL Materials. - 2166-532X. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- Molybdenum clusters, characterized by their unique structure and intriguing catalytic properties, have gained significant attention in recent years. In several existing studies, density functional theory (DFT) methods have been used to find the lowest energy Mo clusters and explore their electronic and magnetic structure. In all cases, with the exception of a single recent study, where a genetic algorithm was employed, initial geometries of the clusters, prior to geometry optimization, were chosen using heuristic approaches based on symmetry considerations and known structures. DFT calculations were performed using different types of pseudopotentials, from soft to hard, and different types of basis sets. However, no comprehensive study has yet been carried out in which a DFT method with the best control on its precision would be complemented by a reliable global minimum search method to find the lowest energy Mo clusters. In this work, we employ a combination of a plane wave-based DFT method and ab initio random structure searching technique to find the lowest energy clusters of up to 10 Mo atoms. In each case, the search has been performed for clusters with different spin multiplicities, which enabled us to explore their magnetic structure. The results are compared for both hard and soft pseudopotentials stressing the importance of treating more electrons explicitly, in agreement with some of the previous studies. For most of the low-energy magnetic structures found, we investigate the distribution of their spin densities, and for all low energy clusters, we confirm their stability by calculating their vibrational structure. For a few smallest clusters, the results of multiconfigurational quantum chemistry calculations are also discussed. Finally, free energies of the Mo clusters, within the quasi-harmonic approximation, are also calculated and discussed.
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| 48. |
- Weser, Oskar, et al.
(författare)
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In Search of the reason for the breathing effect of MIL53 metal-organic framework : An ab initio multiconfigurational study
- 2017
-
Ingår i: Frontiers in Chemistry. - : Frontiers Media SA. - 2296-2646. ; 5:DEC
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Tidskriftsartikel (refereegranskat)abstract
- Multiconfigurational methods are applied to study electronic properties and structural changes in the highly flexible metal-organic framework MIL53(Cr). Via calculated bending potentials of angles, that change the most during phase transition, it is verified that the high flexibility of this material is not a question about special electronic properties in the coordination chemistry, but about overall linking of the framework. The complex posseses a demanding electronic structure with delocalized spin density, antifferomagnetic coupling and high multi-state character requiring multiconfigurational methods. Calculated properties are in good agreement with known experimental values confirming our chosen methods.
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| 49. |
- Widmark, Per Olof, et al.
(författare)
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New compact density matrix averaged ANO basis sets for relativistic calculations
- 2018
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 149:19
-
Tidskriftsartikel (refereegranskat)abstract
- When including relativistic effects in quantum chemical calculations, basis sets optimized for relativistic Hamiltonians such as the atomic natural orbital-relativistic core-correlated (ANO-RCC) basis set have to be used to avoid large errors that appear upon contraction of the basis set. While the large size of the ANO-RCC basis set in terms of primitive basis functions allows for highly accurate calculations, it also hinders its applicability to large sized systems due to the computational costs. To tackle this problem, a new compact relativistic ANO basis set, the ANO-eXtra Small (XS) basis set, is introduced for elements H-Ca. The number of primitive basis functions in ANO-XS is about half that of the ANO-RCC basis set. This greatly reduces the computational costs in the integral calculations especially when used in combination with Cholesky decomposition. At the same time, the ANO-XS basis set is able to predict molecular properties such as bond lengths and excitation energies with reasonable errors compared to the larger ANO-RCC basis set. The main intention for the ANO-XS basis set is to be used in conjunction with the ANO-RCC basis set for large systems that can be divided with regions demanding different qualities of basis sets. This is exemplified in CASPT2 calculations for an Ir(C3H4N)3 complex, where substituting the larger ANO-RCC for the compact ANO-XS basis set at the ligand atoms yields only minor differences for a large number of excited states compared to calculations employing the ANO-RCC basis set on all atoms. Thus, accurate calculations including relativistic effects for large systems become more affordable with the new ANO-XS basis set.
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| 50. |
- Zobel, J. Patrick, et al.
(författare)
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The ANO-R Basis Set
- 2020
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 16:1, s. 278-294
-
Tidskriftsartikel (refereegranskat)abstract
- In this work, the new ANO-R basis set for all elements of the first six periods is introduced. The ANO-R basis set is an all-electron basis set that was constructed including scalar-relativistic effects of the exact-two component (X2C) Hamiltonian and modeling the atomic nucleus by a Gaussian charge distribution, which makes the basis set suitable for calculations of both light and heavy elements. For high accuracy, it takes advantage of the general contraction scheme and was developed at the CASSCF/CASPT2 level of theory. The distinguishing feature of the ANO-R basis set is its compactness in terms of both primitive and contracted basis functions, thus containing no superfluous functions for a given quality. An optimum number of primitive basis functions was selected based on studying the convergence toward the complete basis set limit for each element individually. The primitive basis sets were then contracted using the density-averaged atomic-natural-orbital (ANO) scheme, and suitable contraction levels were determined solely based on the natural orbital occupation numbers that describe the contribution of each natural orbital to the one-particle density matrix. Rather than following the common "split-valence n-tuple zeta plus polarization functions" structure, the resulting basis sets ANO-R0 to ANO-R3 possess a unique composition for each element, ensuring that no unnecessary functions are included while the basis sets are still balanced across the first six periods (H-Rn).
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