| 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
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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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