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Norman, Patrick
Alternative names
Publications (10 of 120) Show all publications
Skånberg, R., Linares, M., König, C., Norman, P., Jönsson, D., Hotz, I. & Ynnerman, A. (2018). VIA-MD: Visual Interactive Analysis of Molecular Dynamics. In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data: . Paper presented at Eurographics Workshop on Visual Computing for Biology and Medicine.
Open this publication in new window or tab >>VIA-MD: Visual Interactive Analysis of Molecular Dynamics
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2018 (English)In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data, 2018Conference paper, Published paper (Refereed)
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-160857 (URN)10.2312/molva.20181102 (DOI)978-3-03868-081-9 (ISBN)
Conference
Eurographics Workshop on Visual Computing for Biology and Medicine
Funder
Swedish Research Council, 2014-4646Swedish National Infrastructure for Computing (SNIC)National Supercomputer Centre (NSC), SwedenEU, European Research Council, 621-2014-4646Swedish e‐Science Research Center
Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2019-10-10
Cukras, J., Kauczor, J., Norman, P., Rizzo, A., Rikken, G. L. J. & Coriani, S. (2016). A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion. Physical Chemistry, Chemical Physics - PCCP, 18(19), 13267-13279
Open this publication in new window or tab >>A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion
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2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 19, p. 13267-13279Article in journal (Refereed) Published
Abstract [en]

A computational protocol for magneto-chiral dichroism and magneto-chiral birefringence dispersion is presented within the framework of damped response theory, also known as complex polarization propagator theory, at the level of time-dependent Hartree-Fock and time-dependent density functional theory. Magneto-chiral dichroism and magneto-chiral birefringence spectra in the (resonant) frequency region below the first ionization threshold of R-methyloxirane and L-alanine are presented and compared with the corresponding results obtained for both the electronic circular dichroism and the magnetic circular dichroism. The additional information content yielded by the magneto-chiral phenomena, as well as their potential experimental detectability for the selected species, is discussed.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2016
National Category
Other Physics Topics
Identifiers
urn:nbn:se:liu:diva-129155 (URN)10.1039/c6cp01465h (DOI)000376138000016 ()27118603 (PubMedID)
Note

Funding Agencies|University of Trieste [CHIM02-Ricerca]; PRIN funding scheme [2009C28YBF_001]; AIAS-COFUND Marie-Curie program [609033]; COST-CMTS Action COnvergent Distributed Environment for Computational Spectroscopy (CODECS) [CM1002]; Interdisciplinary Centre for Mathematical and Computational Modelling (ICM); University of Warsaw [G56-20]

Available from: 2016-06-13 Created: 2016-06-13 Last updated: 2017-11-28
Fahleson, T., Ågren, H. & Norman, P. (2016). A Polarization Propagator for Nonlinear X-ray Spectroscopies. Journal of Physical Chemistry Letters, 7(11), 1991-1995
Open this publication in new window or tab >>A Polarization Propagator for Nonlinear X-ray Spectroscopies
2016 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 11, p. 1991-1995Article in journal (Refereed) Published
Abstract [en]

A complex polarization propagator approach has been developed to third order and implemented in density functional theory (DFT), allowing for the direct calculation of nonlinear molecular properties in the X-ray wavelength regime without explicitly addressing the excited-state manifold. We demonstrate the utility of this propagator method for the modeling of coherent near-edge X-ray two-photon absorption using, as an example, DFT as the underlying electronic structure model. Results are compared with the corresponding near edge X-ray absorption fine structure spectra, illuminating the differences in the role of symmetry, localization, and correlation between the two spectroscopies. The ramifications of this new technique for nonlinear X-ray research are briefly discussed.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2016
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:liu:diva-130066 (URN)10.1021/acs.jpclett.6b00750 (DOI)000377239200009 ()27159130 (PubMedID)
Note

Funding Agencies|Knut and Alice Wallenberg Foundation [KAW-2013.0020]; Swedish Research Council [621-2014-4646]

Available from: 2016-07-06 Created: 2016-07-06 Last updated: 2017-11-28
Fransson, T., Saue, T. & Norman, P. (2016). Four-component damped density functional response theory study of UV/vis absorption spectra and phosphorescence parameters of group 12 metal-substituted porphyrins. Journal of Chemical Theory and Computation, 12(5), 2324-2334
Open this publication in new window or tab >>Four-component damped density functional response theory study of UV/vis absorption spectra and phosphorescence parameters of group 12 metal-substituted porphyrins
2016 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 5, p. 2324-2334Article in journal (Refereed) Published
Abstract [en]

The influences of group 12 (Zn, Cd, Hg) metal-substitution on the valence spectra and phosphorescence parameters of porphyrins (P) have been investigated in a relativistic setting. In order to obtain valence spectra, this study reports the first application of the damped linear response function, or complex polarization propagator, in the four-component density functional theory framework [as formulated in J. Chem. Phys. 133, 064105 (2010)]. It is shown that the steep increase in the density of states as due to the inclusion of spin-orbit coupling yields only minor changes in overall computational costs involved with the solution of the set of linear response equations. Comparing single-frequency to multi-frequency spectral calculations, it is noted that the number of iterations in the iterative linear equation solver per frequency grid-point decreases monotonously from 30 to 0.74 as the number of frequency points goes from one to 19. The main heavy-atom effect on the UV/vis-absorption spectra is indirect and attributed to the change of point group symmetry due to metal-substitution, and it is noted that substitutions using heavier atoms yield small red-shifts of the intense Soret-band. Concerning phosphorescence parameters, the adoption of a four-component relativistic setting enables the calculation of such properties at a linear order of response theory, and any higher-order response functions does not need to be considered. For the substituted porphyrins, electronic coupling between the lowest triplet states is strong and results in theoretical estimates of lifetimes that are sensitive to the wave function and electron density parametrization. With this in mind, we report our best estimates of the phosphorescence lifetimes to be 460, 13.8, 11.2, and 0.00155 s for H2P, ZnP, CdP, and HgP, respectively, with the corresponding transition energies being equal to 1.46, 1.50, 1.38, and 0.89 eV.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-124270 (URN)10.1021/acs.jctc.6b00030 (DOI)000375810000020 ()
Note

Funding agencies: Swedish Research Council [621-2014-4646]

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Available from: 2016-01-25 Created: 2016-01-25 Last updated: 2017-11-30Bibliographically approved
Rinkevicius, Z., Sandberg, J. A. R., Li, X., Linares, M., Norman, P. & Ågren, H. (2016). Hybrid Complex Polarization Propagator/Molecular Mechanics Method for Heterogeneous Environments. Journal of Chemical Theory and Computation, 12(6), 2661-2667
Open this publication in new window or tab >>Hybrid Complex Polarization Propagator/Molecular Mechanics Method for Heterogeneous Environments
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2016 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 6, p. 2661-2667Article in journal (Refereed) Published
Abstract [en]

We introduce a hybrid complex polarization propagator/molecular mechanics method for the calculation of near-resonant and resonant response properties of molecules in heterogeneous environments, which consist of a metallic surface, or nanoparticle, and a solvent. The applicability and performance of the method is demonstrated by computations of linear absorption spectra of p-nitroaniline physisorbed at a gold/dimethyl sulfoxide interface in the UV/vis and near carbon-K-edge regions of the spectrum. It is shown that the shift of absorption cross-section induced by the heterogeneous environment varies significantly depending on the nature,of the excited states encountered in the targeted frequency region as well as on the actual size of the resonant frequencies, and that the solvent component of the heterogeneous environment is responsible for the major part of the environmental shift, especially in the higher frequency range of the carbon K-edge region.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2016
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:liu:diva-130298 (URN)10.1021/acs.jctc.6b00255 (DOI)000378016000015 ()27136079 (PubMedID)
Note

Funding Agencies|Knut and Alice Wallenberg Foundation [KAW-2013.0020]; Swedish e-Science Research Centre (SeRC)

Available from: 2016-07-31 Created: 2016-07-28 Last updated: 2017-11-28
Fransson, T., Burdakova, D. & Norman, P. (2016). K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory. Physical Chemistry, Chemical Physics - PCCP, 18(19), 13591-13603
Open this publication in new window or tab >>K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory
2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 19, p. 13591-13603Article in journal (Refereed) Published
Abstract [en]

X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra—with spin-orbit effects well accounted for—also in cases when the experimental intensity ratio deviate from the statistical one of 1:2. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ~ 1 eV. This anomaly is observed also for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4−XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn–Sham density functional theory (DFT), and to a smaller extent with use of Hartree–Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2016
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-124271 (URN)10.1039/c6cp00561f (DOI)000376138000050 ()
Note

Funding agencies. Knut and Alice Wallenberg Foundation [KAW-2013.0020]; Swedish Research Council [621-2014-4646]

Available from: 2016-01-25 Created: 2016-01-25 Last updated: 2019-12-02Bibliographically approved
Fransson, T., Zhovtobriukh, I., Coriani, S., Wikfeldt, K. T., Norman, P. & Pettersson, L. G. M. (2016). Requirements of first-principles calculations of X-ray absorption spectra of liquid water. Physical Chemistry, Chemical Physics - PCCP, 18(1), 566-583
Open this publication in new window or tab >>Requirements of first-principles calculations of X-ray absorption spectra of liquid water
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2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 1, p. 566-583Article in journal (Refereed) Published
Abstract [en]

A computational benchmark study on X-ray absorption spectra of water has been performed by means of transition-potential density functional theory (TP-DFT), damped time-dependent density functional theory (TDDFT), and damped coupled cluster (CC) linear response theory. For liquid water, using TDDFT with a tailored CAM-B3LYP functional and a polarizable embedding, we find that an embedding with over 2000 water molecules is required to fully converge spectral features for individual molecules, but a substantially smaller embedding can be used within averaging schemes. TP-DFT and TDDFT calculations on 100 MD structures demonstrate that TDDFT produces a spectrum with spectral features in good agreement with experiment, while it is more difficult to fully resolve the spectral features in the TP-DFT spectrum. Similar trends were also observed for calculations of bulk ice. In order to further establish the performance of these methods, small water clusters have been considered also at the CC2 and CCSD levels of theory. Issues regarding the basis set requirements for spectrum simulations of liquid water and the determination of gas-phase ionization potentials are also discussed.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2016
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-124266 (URN)10.1039/C5CP03919C (DOI)000368755500059 ()26619162 (PubMedID)
Note

Funding agencies: Swedish Research Council [621-2014-4646, 621-2011-4223]; Knut and Alice Wallenberg Foundation [KAW-2013.0020]

Available from: 2016-01-25 Created: 2016-01-25 Last updated: 2017-11-30Bibliographically approved
Shirani, H., Linares, M., Sigurdson, C. J., Lindgren, M., Norman, P. & Nilsson, P. (2015). A Palette of Fluorescent Thiophene-Based Ligands for the Identification of Protein Aggregates. Chemistry - A European Journal, 21(43), 15133-15137
Open this publication in new window or tab >>A Palette of Fluorescent Thiophene-Based Ligands for the Identification of Protein Aggregates
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2015 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 43, p. 15133-15137Article in journal (Refereed) Published
Abstract [en]

By replacing the central thiophene unit of an anionic pentameric oligothiophene with other heterocyclic moities, a palette of pentameric thiophene-based ligands with distinct fluorescent properties were synthesized. All ligands displayed superior selectivity towards recombinant amyloid fibrils as well as disease-associated protein aggregates in tissue sections.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2015
Keywords
Alzheimers disease; fluorescent probes; luminescence; oligothiophenes; microscopy
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-122776 (URN)10.1002/chem.201502999 (DOI)000363332200011 ()26388448 (PubMedID)
Note

Funding Agencies|Swedish Foundation for Strategic Research; Erling Persson foundation; Alzheimers Disease Research Center (NIH) [AGO 5131]; ERC from the European Research Council; Swedish e-Science Research Center (SeRC); Swedish Research Council [621-2014-4646]

Available from: 2015-11-23 Created: 2015-11-23 Last updated: 2017-12-01
Holmgaard List, N., Kauczor, J., Saue, T., Jorgen Aagaard Jensen, H. & Norman, P. (2015). Beyond the electric-dipole approximation: A formulation and implementation of molecular response theory for the description of absorption of electromagnetic field radiation. Journal of Chemical Physics, 142(24), 244111
Open this publication in new window or tab >>Beyond the electric-dipole approximation: A formulation and implementation of molecular response theory for the description of absorption of electromagnetic field radiation
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2015 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 142, no 24, p. 244111-Article in journal (Refereed) Published
Abstract [en]

We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2015
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-120463 (URN)10.1063/1.4922697 (DOI)000357615100015 ()26133414 (PubMedID)
Note

Funding Agencies|Lundbeck Foundation; Danish Council for Independent Research; Knut and Alice Wallenberg Foundation [KAW-2013.0020]; Swedish Research Council [621-2014-4646]

Available from: 2015-08-12 Created: 2015-08-11 Last updated: 2017-12-04
Rubio-Magnieto, J., Di Meo, F., Lo, M., Delcourt, C., Clement, S., Norman, P., . . . Surin, M. (2015). Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes. Organic and biomolecular chemistry, 13(8), 2453-2463
Open this publication in new window or tab >>Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes
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2015 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 8, p. 2453-2463Article in journal (Refereed) Published
Abstract [en]

The molecular recognition of human telomeric G-quadruplexes by a novel cationic pi-extended Ni-II-porphyrin (Ni-II-TImidP4) is studied in aqueous solutions via (chir) optical spectroscopy, Fluorescence Resonance Energy Transfer (FRET) melting assay, and computational molecular modeling. The results are systematically compared with the recognition by a conventional meso-substituted Ni-II-porphyrin (Ni-II-TMPyP4), which allows us to pinpoint the differences in binding modes depending on the G-quadruplex topology. Importantly, FRET melting assays show the higher selectivity of Ni-II-TImidP4 towards human telomeric G4 than that of Ni-II-TMPyP4.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2015
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-115832 (URN)10.1039/c4ob02097a (DOI)000349669300033 ()25563845 (PubMedID)
Note

Funding Agencies|Fonds de la Recherche Scientifique-FNRS (Belgium) [2.4615.11-BINDER]; SeRC (Swedish e-Science Research Center); Swedish Research Council [621-2010-5014]; CNRS; Agence Nationale de la Recherche (ANR) [ANR-09-JCJC-0089-01]

Available from: 2015-03-20 Created: 2015-03-20 Last updated: 2017-12-04
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