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Ågren, H., Harczuk, I. & Vahtras, O. (2019). Decomposition of molecular properties. Physical Chemistry, Chemical Physics - PCCP, 21(5), 2251-2270
Open this publication in new window or tab >>Decomposition of molecular properties
2019 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 5, p. 2251-2270Article in journal (Refereed) Published
Abstract [en]

We review recent work on property decomposition techniques using quantum emical methods and discuss some topical applications in terms of antum mechanics-molecular mechanics calculations and the constructing properties of large molecules and clusters. Starting out from the -called LoProp decomposition scheme [Gagliardi et al., J. Chem. Phys., 04, 121, 4994] for extracting atomic and inter-atomic contributions to lecular properties we show how this method can be generalized to calized frequency-dependent polarizabilities, to localized perpolarizabilities and to localized dispersion coefficients. Some plications of the generalized decomposition technique are reviewed - lculations of frequency-dependent polarizabilities, Rayleigh attering of large clusters, and calculations of hyperpolarizabilities proteins.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2019
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-248360 (URN)10.1039/c8cp04340j (DOI)000461667900003 ()30663732 (PubMedID)2-s2.0-85060820802 (Scopus ID)
Note

QC 20190405

Available from: 2019-04-05 Created: 2019-04-05 Last updated: 2019-04-05Bibliographically approved
Rinkevicius, Z., Xin, L., Vahtras, O., Brand, M., Ahmadzadeh, K., Ringholm, M., . . . Norman, P. (2019). New and efficient Python/C plus plus modular library for real and complex response functions at the level of Kohn-Sham density functional theory. Paper presented at 257th National Meeting of the American-Chemical-Society (ACS), MAR 31-APR 04, 2019, Orlando, FL. Abstracts of Papers of the American Chemical Society, 257
Open this publication in new window or tab >>New and efficient Python/C plus plus modular library for real and complex response functions at the level of Kohn-Sham density functional theory
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2019 (English)In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 257Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
American Chemical Society (ACS), 2019
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-257663 (URN)000478861204497 ()
Conference
257th National Meeting of the American-Chemical-Society (ACS), MAR 31-APR 04, 2019, Orlando, FL
Note

QC 20190904

Available from: 2019-09-04 Created: 2019-09-04 Last updated: 2019-09-04Bibliographically approved
Nørby, M. S., Vahtras, O., Norman, P. & Kongsted, J. (2017). Assessing frequency-dependent site polarisabilities in linear response polarisable embedding. Molecular Physics, 115, 39-47
Open this publication in new window or tab >>Assessing frequency-dependent site polarisabilities in linear response polarisable embedding
2017 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, p. 39-47Article in journal (Refereed) Published
Abstract [en]

In this paper, we discuss the impact of using a frequency-dependent embedding potential in quantum chemical embedding calculations of response properties. We show that the introduction of a frequency-dependent embedding potential leads to further model complications upon solving the central equations defining specific molecular properties. On the other hand, we also show from a numerical point of view that the consequences of using such a frequency-dependent embedding potential is almost negligible. Thus, for the kind of systems and processes studied in this paper the general recommendation is to use frequency-independent embedding potentials since this leads to less complicated model issues. However, larger effects are expected if the absorption bands of the environment are closer to that of the region treated using quantum mechanics.

Place, publisher, year, edition, pages
Taylor & Francis, 2017
Keywords
distributed polarisabilities, Frequency-dependent embedding potential, QM/MM embedding, response properties, Quantum theory, Frequency dependent, Frequency independent, Molecular properties, Polarisabilities, Quantum chemical, Systems and process, Quantum chemistry
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-198703 (URN)10.1080/00268976.2016.1177667 (DOI)000396794700006 ()2-s2.0-84966589329 (Scopus ID)
Note

QC 20161222

Available from: 2016-12-22 Created: 2016-12-21 Last updated: 2017-11-29Bibliographically approved
Zagorodskikh, S., Vapa, M., Vahtras, O., Zhaunerchyk, V., Mucke, M., Eland, J. H., . . . Feifel, R. (2016). An experimental and theoretical study of core-valence double ionisation of acetaldehyde (ethanal). Physical Chemistry, Chemical Physics - PCCP, 18(4), 2535-2547
Open this publication in new window or tab >>An experimental and theoretical study of core-valence double ionisation of acetaldehyde (ethanal)
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2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 4, p. 2535-2547Article in journal (Refereed) Published
Abstract [en]

Core-valence double ionisation spectra of acetaldehyde (ethanal) are presented at photon energies above the carbon and oxygen 1s ionisation edges, measured by a versatile multi-electron coincidence spectroscopy technique. We use this molecule as a testbed for analyzing core-valence spectra by means of quantum chemical calculations of transition energies. These theoretical approaches range from two simple models, one based on orbital energies corrected by core valence interaction and one based on the equivalent core approximation, to a systematic series of quantum chemical electronic structure methods of increasing sophistication. The two simple models are found to provide a fast orbital interpretation of the spectra, in particular in the low energy parts, while the coverage of the full spectrum is best fulfilled by correlated models. CASPT2 is the most sophisticated model applied, but considering precision as well as computational costs, the single and double excitation configuration interaction model seems to provide the best option to analyze core-valence double hole spectra.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2016
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-183675 (URN)10.1039/c5cp05758b (DOI)000369506000030 ()26700657 (PubMedID)2-s2.0-84955271543 (Scopus ID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC), SNIC 023/07-18
Note

QC 20160319

Available from: 2016-03-19 Created: 2016-03-18 Last updated: 2017-11-30Bibliographically approved
Harczuk, I., Vahtras, O. & Ågren, H. (2016). Hyperpolarizabilities of extended molecular mechanical systems. Physical Chemistry, Chemical Physics - PCCP, 18(12), 8710-8722
Open this publication in new window or tab >>Hyperpolarizabilities of extended molecular mechanical systems
2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 12, p. 8710-8722Article in journal (Refereed) Published
Abstract [en]

We propose and evaluate algorithms for the calculation of molecular polarizabilities and hyperpolarizabilities of extended chemical systems. These algorithms are generalizations of the Silberstein-Applequist procedure involving interacting induced classical dipoles through the localized polarizabilities and hyperpolarizabilities. The models are evaluated in terms of interacting molecular units as well as interacting atomic units that result from the atomic decomposition scheme known as the LoProp transformation. We introduce a generalized LoProp scheme which applies to hyperpolarizabilities as well as to polarizabilities. The accuracy of the second-order Applequist method is tested for the first hyperpolarizability for the TIP3P water model using both Hartree-Fock and density functional theory evaluated with different basis sets. Possible applications and ramifications of the scheme are discussed.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2016
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-187159 (URN)10.1039/c5cp06688c (DOI)2-s2.0-84961843157 (Scopus ID)
Funder
Swedish National Infrastructure for Computing (SNIC), 023/07-18Swedish National Infrastructure for Computing (SNIC), 2015-1-230
Note

QC 20160518

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2019-10-02Bibliographically approved
Harczuk, I., Vahtras, O. & Ågren, H. (2016). Modeling Rayleigh Scattering of Aerosol Particles. Journal of Physical Chemistry B, 120(18), 4296-4301
Open this publication in new window or tab >>Modeling Rayleigh Scattering of Aerosol Particles
2016 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 18, p. 4296-4301Article in journal (Refereed) Published
Abstract [en]

Rayleigh scattering of naturally polarized lightwas studied for systems with atmospheric relevance represent-ing growing water clusters with adsorbed cis-pinonic acid. Thescattering intensity was computed from the static anddynamical polarizabilities of the clusters obtained by a recentlyderived methodology for classical polarizabilities, in whichApplequist equations for interacting polarizable dipoles areused together with point-dipoles and polarizabilities obtainedby quantum chemistry and decomposed into the atomicdomain by the so-called LoProp transformation generalized forfrequency dependence. The Applequist interaction was foundto yield scattering intensities 20% larger for a cluster consistingof 1000 water molecules, as compared to the method where allof the polarizabilities of molecules are added withoutinteractions. It was confirmed that scattering intensity depends quadratically on the number of water molecules in the cluster,and that it also increases quadratically with increase in the mass constituent of the foreign substance. The adsorption of the cis-pinonic acid increases the contribution to the scattering intensity stemming from the anisotropic polarizability, as compared tothe isotropic contribution. The ramifications of the method in predicting Rayleigh scattering and the earth’s albedo with respectto man-made and natural gas emission are briefly discussed.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-187164 (URN)10.1021/acs.jpcb.6b02278 (DOI)000375968900012 ()2-s2.0-84969924848 (Scopus ID)
Funder
Swedish National Infrastructure for Computing (SNIC), 023/07-18Swedish National Infrastructure for Computing (SNIC), 2015-1-230
Note

QC 20160518

Available from: 2016-05-17 Created: 2016-05-17 Last updated: 2017-11-30Bibliographically approved
Harczuk, I., Vahtras, O. & Ågren, H. (2015). Frequency-dependent force fields for QMMM calculations. Physical Chemistry, Chemical Physics - PCCP, 17(12), 7800-7812
Open this publication in new window or tab >>Frequency-dependent force fields for QMMM calculations
2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 12, p. 7800-7812Article in journal (Refereed) Published
Abstract [en]

We outline the construction of frequency-dependent polarizable force fields. The force fields are derived from analytic response theory for different frequencies using a generalization of the LoProp algorithm giving a decomposition of a molecular dynamical polarizability to localized atomic dynamical polarizabilities. These force fields can enter in a variety of applications - we focus on two such applications in this work: firstly, they can be incorporated in a physical, straightforward, way for current existing methods that use polarizable embeddings, and we can show, for the first time, the effect of the frequency dispersion within the classical environment of a quantum mechanics-molecular mechanics (QMMM) method. Our methodology is here evaluated for some test cases comprising water clusters and organic residues. Secondly, together with a modified Silberstein-Applequist procedure for interacting inducible point-dipoles, these frequency-dependent polarizable force fields can be used for a classical determination of frequency-dependent cluster polarizabilities. We evaluate this methodology by comparing with the corresponding results obtained from quantum mechanics or QMMM where the absolute mean (alpha) over bar is determined with respect to the size of the QM and MM parts of the total system.

National Category
Atom and Molecular Physics and Optics Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-165243 (URN)10.1039/c4cp05411c (DOI)000351437500025 ()25714984 (PubMedID)2-s2.0-84924871325 (Scopus ID)
Note

QC 20150504

Available from: 2015-05-04 Created: 2015-04-24 Last updated: 2017-12-04Bibliographically approved
Löytynoja, T., Niskanen, J., Jankala, K., Vahtras, O., Rinkevicius, Z. & Ågren, H. (2014). Quantum Mechanics/Molecular Mechanics Modeling of Photoelectron Spectra: The Carbon 1s Core-Electron Binding Energies of Ethanol-Water Solutions. Journal of Physical Chemistry B, 118(46), 13217-13225
Open this publication in new window or tab >>Quantum Mechanics/Molecular Mechanics Modeling of Photoelectron Spectra: The Carbon 1s Core-Electron Binding Energies of Ethanol-Water Solutions
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2014 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 46, p. 13217-13225Article in journal (Refereed) Published
Abstract [en]

Using ethanolwater solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solutesolvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics modelelectrostatic, polarization, and van der Waalswith atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

National Category
Theoretical Chemistry Physical Sciences
Identifiers
urn:nbn:se:kth:diva-158401 (URN)10.1021/jp506410w (DOI)000345468600021 ()2-s2.0-84912530091 (Scopus ID)
Note

QC 20150109

Available from: 2015-01-09 Created: 2015-01-07 Last updated: 2018-04-27Bibliographically approved
Harczuk, I., Murugan, N. A., Vahtras, O. & Agren, H. (2014). Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field. Journal of Chemical Theory and Computation, 10(8), 3492-3502
Open this publication in new window or tab >>Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field
2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 8, p. 3492-3502Article in journal (Refereed) Published
Abstract [en]

The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environment electronic embedding and polarizable electronic embedding accounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-150932 (URN)10.1021/ct5001318 (DOI)000340351200059 ()2-s2.0-84906236526 (Scopus ID)
Note

QC 20140912

Available from: 2014-09-12 Created: 2014-09-11 Last updated: 2017-12-05Bibliographically approved
Aidas, K., Angeli, C., Bak, K. L., Bakken, V., Bast, R., Boman, L., . . . Ågren, H. (2014). The Dalton quantum chemistry program system. Wiley Interdisciplinary Reviews. Computational Molecular Science, 4(3), 269-284
Open this publication in new window or tab >>The Dalton quantum chemistry program system
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2014 (English)In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, no 3, p. 269-284Article in journal (Refereed) Published
Abstract [en]

Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

Keywords
Self-Consistent-Field, Density-Functional Theory, Coupled-Cluster Singles, Polarizable Continuum Model, Response Theory Calculations, London Atomic Orbitals, Ab-Initio Calculations, Frequency-Dependent Polarizabilities, Plesset Perturbation-Theory, Natural Circular-Dichroism
National Category
Bioinformatics (Computational Biology) Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-145261 (URN)10.1002/wcms.1172 (DOI)000334522200006 ()2-s2.0-84898548879 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20140516

Available from: 2014-05-16 Created: 2014-05-15 Last updated: 2018-01-11Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9123-8174

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