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Publications (10 of 18) Show all publications
Hodecker, M., Rehn, D. R., Norman, P. & Dreuw, A. (2019). Algebraic-diagrammatic construction scheme for the polarization propagator including ground-state coupled-cluster amplitudes. II. Static polarizabilities. Journal of Chemical Physics, 150(17), Article ID 174105.
Open this publication in new window or tab >>Algebraic-diagrammatic construction scheme for the polarization propagator including ground-state coupled-cluster amplitudes. II. Static polarizabilities
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 17, article id 174105Article in journal (Refereed) Published
Abstract [en]

The modification of the algebraic-diagrammatic construction (ADC) scheme for the polarization propagator using ground-state coupled-cluster (CC) instead of Møller-Plesset (MP) amplitudes, referred to as CC-ADC, is extended to the calculation of molecular properties, in particular, dipole polarizabilities. Furthermore, in addition to CC with double excitations (CCD), CC with single and double excitations (CCSD) amplitudes can be used, also in the second-order transition moments of the ADC(3/2) method. In the second-order CC-ADC(2) variants, the MP correlation coefficients occurring in ADC are replaced by either CCD or CCSD amplitudes, while in the F/CC-ADC(2) and F/CC-ADC(3/2) variants, they are replaced only in the second-order modified transition moments. These newly implemented variants are used to calculate the static dipole polarizability of several small- to medium-sized molecules, and the results are compared to the ones obtained by full configuration interaction or experiment. It is shown that the results are consistently improved by the use of CC amplitudes, in particular, for aromatic systems such as benzene or pyridine, which have proven to be difficult cases for standard ADC approaches. In this case, the second-order CC-ADC(2) and F/CC-ADC(2) variants yield significantly better results than the standard third-order ADC(3/2) method, at a computational cost amounting to only about 1% of the latter.

Place, publisher, year, edition, pages
American Institute of Physics Inc., 2019
Keywords
Algebra, Cluster analysis, Ground state, Polarization, Algebraic diagrammatic constructions, Correlation coefficient, Dipole polarizabilities, Full configuration interaction, Medium-sized molecules, Second order transition, Static dipole polarizabilities, Static polarizabilities, Numerical methods
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-252468 (URN)10.1063/1.5081665 (DOI)000467255500005 ()2-s2.0-85065146754 (Scopus ID)
Note

QC 20190715

Available from: 2019-07-15 Created: 2019-07-15 Last updated: 2019-07-15Bibliographically approved
Brumboiu, I., Eriksson, O. & Norman, P. (2019). Atomic photoionization cross sections beyond the electric dipole approximation. Journal of Chemical Physics, 150(4), Article ID 044306.
Open this publication in new window or tab >>Atomic photoionization cross sections beyond the electric dipole approximation
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 4, article id 044306Article in journal (Refereed) Published
Abstract [en]

A methodology is developed to compute photoionization cross sections beyond the electric dipole approximation from response theory, using Gaussian type orbitals and plane waves for the initial and final states, respectively. The methodology is applied to compute photoionization cross sections of atoms and ions from the first four rows of the periodic table. Analyzing the error due to the plane wave description of the photoelectron, we find kinetic energy and concomitant photon energy thresholds above which the plane wave approximation becomes applicable. The correction introduced by going beyond the electric dipole approximation increases with photon energy and depends on the spatial extension of the initial state. In general, the corrections are below 10% for most elements, at a photon energy reaching up to 12 keV. 2019 Author(s).

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2019
Keywords
LEUZE M, 1994, MOLECULAR PHYSICS, V83, P655
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-244111 (URN)10.1063/1.5083649 (DOI)000457414600056 ()30709292 (PubMedID)2-s2.0-85060862106 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish Research Council, 621-2014-4646
Note

QC 20190219

Available from: 2019-02-19 Created: 2019-02-19 Last updated: 2019-02-19Bibliographically approved
Linares, M., Sun, H., Biler, M., Andreasson, J. & Norman, P. (2019). Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra. Physical Chemistry, Chemical Physics - PCCP, 21(7), 3637-3643
Open this publication in new window or tab >>Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra
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2019 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 7, p. 3637-3643Article in journal (Refereed) Published
Abstract [en]

DNA binding modes of the stereoisomeric rotamers of two dithenylethene derivatives (DTE1 and DTE2) representing candidate molecular photoswitches of great promise for photopharmacology and nanotechnology have been identified and characterized in terms of their binding energies and electronic circular dichroism (CD) responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of methyl groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall negative linear dichroism (LD) as observed in the experiment for DTE1 (Angew. Chem., Int. Ed., 2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a positive theoretical signature CD band in the long wavelength region with origin in pyridinium ligands. The theoretical CD spectrum is found to be in good agreement with the experimental one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-246264 (URN)10.1039/c8cp05326j (DOI)000459585900024 ()30379159 (PubMedID)2-s2.0-85061512565 (Scopus ID)
Note

QC 20190326

Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-03-26Bibliographically approved
Cornelissen, T. D., Biler, M., Urbanaviciute, I., Norman, P., Linares, M. & Kemerink, M. (2019). Kinetic Monte Carlo simulations of organic ferroelectrics. Physical Chemistry, Chemical Physics - PCCP, 21(3), 1375-1383
Open this publication in new window or tab >>Kinetic Monte Carlo simulations of organic ferroelectrics
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2019 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 3, p. 1375-1383Article in journal (Refereed) Published
Abstract [en]

Ferroelectrics find broad applications, e.g. in non-volatile memories, but the switching kinetics in real, disordered, materials is still incompletely understood. Here, we develop an electrostatic model to study ferroelectric switching using 3D Monte Carlo simulations. We apply this model to the prototypical small molecular ferroelectric trialkylbenzene-1,3,5-tricarboxamide (BTA) and find good agreement between the Monte Carlo simulations, experiments, and molecular dynamics studies. Since the model lacks any explicit steric effects, we conclude that these are of minor importance. While the material is shown to have a frustrated antiferroelectric ground state, it behaves as a normal ferroelectric under practical conditions due to the large energy barrier for switching that prevents the material from reaching its ground state after poling. We find that field-driven polarization reversal and spontaneous depolarization have orders of magnitude different switching kinetics. For the former, which determines the coercive field and is relevant for data writing, nucleation occurs at the electrodes, whereas for the latter, which governs data retention, nucleation occurs at disorder-induced defects. As a result, by reducing the disorder in the system, the polarization retention time can be increased dramatically while the coercive field remains unchanged.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-243951 (URN)10.1039/c8cp06716c (DOI)000456147000040 ()30601493 (PubMedID)2-s2.0-85060120855 (Scopus ID)
Note

QC 20190304

Available from: 2019-03-04 Created: 2019-03-04 Last updated: 2019-03-12Bibliographically approved
Sun, H., Lingyi, Z., Norman, P. & Weibing, Z. (2019). Molecular Dynamic of Various DNA Sequences Binding of Dithienylethenest. Gaodeng xuéxiào huàxué xuébào, 40(6), 1229-1235
Open this publication in new window or tab >>Molecular Dynamic of Various DNA Sequences Binding of Dithienylethenest
2019 (English)In: Gaodeng xuéxiào huàxué xuébào, ISSN 0251-0790, Vol. 40, no 6, p. 1229-1235Article in journal (Refereed) Published
Abstract [en]

Binding modes between various DNA sequences and stereoisomeric rotamers of two dithienylethene derivatives (DTE1 and DTE2) representing photochromic switches were investigated in terms of molecular dynamics simulations and characterized by their binding energies. The result shows that minor groove binding (MiGB) is found to be the most robust binding mode between DNA and DTE (either DTE1 or DTE2). Due to steric hindrance, two DTE derivatives that are rotatable isomers exhibit distinct binding behaviors to DNA, and thus DNA has significant enantioselectivity for DTE derivatives. Moreover, the selectivity of the DTE derivative to the binding site of the DNA molecule is directly related to the base pair constitution, providing accurate theoretical guidance for precision medicine by chiral drugs based on this molecule.

Place, publisher, year, edition, pages
Higher Education Press, 2019
Keywords
Molecular dynamics, Chiral drug, Dithienylethene, DNA, Rotamer, Binding mode
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-262998 (URN)10.7503/cjcu20180837 (DOI)000489907700018 ()2-s2.0-85070523702 (Scopus ID)
Note

QC 20191031

Available from: 2019-10-31 Created: 2019-10-31 Last updated: 2019-11-13Bibliographically approved
Brumboiu, I. E., Eriksson, O. & Norman, P. (2019). Photoelectron Spectroscopy of Molecules Beyond the Electric Dipole Approximation. Journal of Chemical Theory and Computation, 15(10), 5483-5494
Open this publication in new window or tab >>Photoelectron Spectroscopy of Molecules Beyond the Electric Dipole Approximation
2019 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 10, p. 5483-5494Article in journal (Refereed) Published
Abstract [en]

A methodology implemented to compute photoionization cross sections beyond the electric dipole approximation using Gaussian type orbitals for the initial state and plane waves for the final state is applied to molecules of various sizes. The molecular photoionization cross sections computed for valence molecular orbitals as a function of photon energy present oscillations due to the wave-like nature of both the outgoing photoelectron and of the incoming photon. These oscillations are damped by rotational and vibrational averaging or by performing a k-point summation for the solid state case. For core orbitals, the corrections introduced by going beyond the electric dipole approximation are comparable to the atomic case. For valence orbitals, nondipole corrections to the total photoinization cross sections can reach up to 20% at photon energies above 1 keV. The corrections to the differential cross sections calculated at the magic angle are larger, reaching values between 30% and 50% for all molecules included. Our findings demonstrate that photoelectron spectroscopy, especially angle-resolved, on, e.g., molecules and clusters on surfaces, using high photon energies, must be accompanied by theories that go beyond the electric dipole approximation.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2019
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-262957 (URN)10.1021/acs.jctc.9b00470 (DOI)000489678700028 ()31509709 (PubMedID)2-s2.0-85072975282 (Scopus ID)
Note

QC 20191203

Available from: 2019-12-03 Created: 2019-12-03 Last updated: 2019-12-03Bibliographically approved
Urbanaviciute, I., Bhattacharjee, S., Biler, M., Lugger, J. A. M., Cornelissen, T. D., Norman, P., . . . Kemerink, M. (2019). Suppressing depolarization by tail substitution in an organic supramolecular ferroelectric. Physical Chemistry, Chemical Physics - PCCP, 21(4), 2069-2079
Open this publication in new window or tab >>Suppressing depolarization by tail substitution in an organic supramolecular ferroelectric
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2019 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 4, p. 2069-2079Article in journal (Refereed) Published
Abstract [en]

Despite being very well established in the field of electro-optics, ferroelectric liquid crystals so far lacked interest from a ferroelectric device perspective due to a typically high operating temperature, a modest remnant polarization and/or poor polarization retention. Here, we experimentally demonstrate how simple structural modification of a prototypical ferroelectric liquid-crystal benzene-1,3,5-trisamide (BTA) - introduction of branched-tail substituents - results in materials with a wide operating temperature range and a data retention time of more than 10 years in thin-film solution-processed capacitor devices at room temperature. The observed differences between linear- and branched-tail compounds are analyzed using density functional theory (DFT) and molecular dynamics (MD) simulations. We conclude that morphological factors like improved packing quality and reduced disorder, rather than electrostatic interactions or intra/inter-columnar steric hindrance, underlay the superior properties of the branched-tailed BTAs. Synergistic effects upon blending of compounds with branched and linear side-chains can be used to further improve the materials' characteristics.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-246286 (URN)10.1039/c8cp06315j (DOI)000459584100039 ()30638230 (PubMedID)2-s2.0-85060382616 (Scopus ID)
Note

QC 20190325

Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-03-25Bibliographically approved
Zhovtobriukh, I., Norman, P. & Pettersson, L. G. M. (2019). X-ray absorption spectrum simulations of hexagonal ice. Journal of Chemical Physics, 150(3), Article ID 034501.
Open this publication in new window or tab >>X-ray absorption spectrum simulations of hexagonal ice
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 3, article id 034501Article in journal (Refereed) Published
Abstract [en]

We calibrate basis sets and performance of two theoretical approaches to compute X-ray absorption spectra (XAS) of condensed water by comparison to experiments on hexagonal ice Ih. We apply both the transition-potential half-core-hole approach and the complex polarization propagator using four different models of the crystal with increasing oxygen and proton disorder but find poor agreement with experiments. We note that there are large variations in experimental spectra depending on detection mode and how the ice samples were prepared, which leads us to critically investigate what structures were actually prepared and measured in each case. This is done by using a Monte Carlo-based fitting technique which fits the spectra based on a library of precomputed spectra and assigns weights to contributions from different model structures. These are then used to generate O-O and O-H radial distribution functions and tetrahedrality parameters associated with each of the measured spectra. We find that all spectra are associated with sharp peaks at the oxygen positions in the perfect lattice, but with significant disorder around these positions. We suggest that presently available XAS of hexagonal ice are not fully representative of the perfect crystalline lattice, but contain varying amounts of defects and possible contributions from low-density amorphous ice.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2019
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-243950 (URN)10.1063/1.5078385 (DOI)000456266100016 ()30660146 (PubMedID)2-s2.0-85060175783 (Scopus ID)
Note

QC 20190305

Available from: 2019-03-05 Created: 2019-03-05 Last updated: 2019-03-05Bibliographically approved
König, C., Skanberg, R., Hotz, I., Ynnerman, A., Norman, P. & Linares, M. (2018). Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations. Chemical Communications, 54(24), 3030-3033
Open this publication in new window or tab >>Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations
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2018 (English)In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 24, p. 3030-3033Article in journal (Refereed) Published
Abstract [en]

A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2018
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-225707 (URN)10.1039/c8cc00105g (DOI)000428086500019 ()29512664 (PubMedID)2-s2.0-85044199897 (Scopus ID)
Funder
Swedish e‐Science Research CenterSwedish Research Council, 621-2014-4646
Note

QC 20180411

Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-04-11Bibliographically approved
Norman, P., Ruud, K. & Saue, T. (2018). Principles and practices of molecular properties: Theory, modeling and simulations. Wiley
Open this publication in new window or tab >>Principles and practices of molecular properties: Theory, modeling and simulations
2018 (English)Book (Other academic)
Abstract [en]

A comprehensive yet accessible exploration of quantum chemical methods for the determination of molecular properties of spectroscopic relevance Molecular properties can be probed both through experiment and simulation. This book bridges these two worlds, connecting the experimentalist's macroscopic view of responses of the electromagnetic field to the theoretician's microscopic description of the molecular responses. Comprehensive in scope, it also offers conceptual illustrations of molecular response theory by means of time-dependent simulations of simple systems. This important resource in physical chemistry offers: A journey in electrodynamics from the molecular microscopic perspective to the conventional macroscopic viewpoint The construction of Hamiltonians that are appropriate for the quantum mechanical description of molecular properties Time- and frequency-domain perspectives of light-matter interactions and molecular responses of both electrons and nuclei An introduction to approximate state response theory that serves as an everyday tool for computational chemists A unified presentation of prominent molecular properties Principles and Practices of Molecular Properties: Theory, Modeling and Simulations is written by noted experts in the field. It is a guide for graduate students, postdoctoral researchers and professionals in academia and industry alike, providing a set of keys to the research literature. 

Place, publisher, year, edition, pages
Wiley, 2018
Series
Principles and Practices of Molecular Properties: Theory, Modeling and Simulations
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-236782 (URN)10.1002/9781118794821 (DOI)2-s2.0-85050296383 (Scopus ID)9781118794821 (ISBN)9780470725627 (ISBN)
Note

QC 20190109

Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-03-18Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-1191-4954

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