| 1. |
- Abrikosov, Alexei I., et al.
(author)
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Multiscale study of crystal and electronic structure of Al defects in concrete
- 2018
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In: International Conference of Computational Methods in Sciences and Engineering 2018, ICCMSE 2018. - : Author(s). - 9780735417663 ; 2040
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Conference paper (peer-reviewed)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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| 2. |
- Aquilante, Francesco, et al.
(author)
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Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table
- 2016
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In: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 506-541
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Journal article (peer-reviewed)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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| 3. |
- Bolaño, Iria, et al.
(author)
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Pyridine-cyanoanthracene bonded exciplex
- 2019
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In: 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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Conference paper (peer-reviewed)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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| 4. |
- Bywater, Robert P, et al.
(author)
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The dipeptide conformations of all twenty amino acid types in the context of biosynthesis.
- 2015
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In: SpringerPlus. - : Springer Science and Business Media LLC. - 2193-1801. ; 4
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Journal article (peer-reviewed)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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| 5. |
- Galván, Ignacio Fdez., et al.
(author)
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OpenMolcas : From Source Code to Insight
- 2019
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Journal article (peer-reviewed)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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| 6. |
- Johansson, Marcus, et al.
(author)
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Automatic procedure for generating symmetry adapted wavefunctions
- 2017
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In: Journal of Cheminformatics. - : Springer Science and Business Media LLC. - 1758-2946. ; 9:1
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Journal article (peer-reviewed)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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| 7. |
- Kovacevic, Goran, et al.
(author)
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Atomistic modeling of crystal structure of Ca1.67SiHx
- 2015
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In: Cement and Concrete Research. - : Elsevier BV. - 0008-8846. ; 67, s. 197-203
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Journal article (peer-reviewed)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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| 8. |
- Kovačević, Goran, et al.
(author)
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Luscus: molecular viewer and editor for MOLCAS.
- 2015
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In: Journal of Cheminformatics. - : Springer Science and Business Media LLC. - 1758-2946. ; 7, s. 16-16
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Journal article (peer-reviewed)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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| 9. |
- Kovačević, Goran, et al.
(author)
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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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In: Zeitschrift fur Physikalische Chemie. - : Walter de Gruyter GmbH. - 0942-9352 .- 2196-7156. ; 230:9, s. 1411-1424
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Journal article (peer-reviewed)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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| 10. |
- Naderi, Fereshteh, et al.
(author)
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Multiconfigurational Study of the Electronic Structure of Negatively Charged Fullerens
- 2017
-
In: Journal of Chemistry and Chemical Engineering. - : David Publishing Company. - 1934-7375 .- 1934-7383. ; 11, s. 30-30
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Journal article (peer-reviewed)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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