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Derivation and application of response functions for nonlinear absorption and dichroisms
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is titled ’Derivation and application of response functions for nonlinear absorption and dichroisms’ and was written by Tobias Fahleson at the Division of Theoretical Chemistry & Biology at KTH Royal Institute of Technology in Sweden. It explores and expands upon theoretical means of quantifying a number of nonlinear spectroscopies, including two-photon absorption, resonant inelastic x-ray scattering, Jones birefringence, and magnetic circular dichroism. Details are provided for the derivation and program implementation of complex-valued (damped) cubic response functions that have been implemented in the quantum chemistry package DALTON [1], based on working equations formulated for an approximate-state wave function. This is followed by an assessment of the implementation. It is demonstrated how two-photon absorption (TPA) can be described either through second-order transition moments or the damped cubic response function. A set of illustrative TPA profiles are produced for smaller molecules. In addition, resonant inelastic x-ray scattering (RIXS) is explored in a similar manner as two-photon absorption. It is shown for small systems how RIXS spectra may be obtained using a reduced form of the cubic response function. Linear birefringences are investigated for noble gases, monosubstituted benzenes, furan homologues, and liquid acetonitrile. Regarding the noble gases, the Jones effect is shown to be proportional to a power series with respect to atomic radial sizes. For monosubstituted benzenes, a linear relation between the Jones birefringence and the empirical para-Hammett constant as well as the permanent electric dipole moment is presented. QM/MM protocols are applied for a pure acetonitrile liquid, including polarizable embedding and polarizable-density embedding models. The final chapter investigates magnetically induced circular dichroism (MCD). A question regarding relative stability of the first set of excited states for DNA-related molecular systems is resolved through MCD by exploiting the signed nature of circular dichroisms. Furthermore, to what extent solvent contributions affect MCD spectra and the effect on uracil MCD spectrum due to thionation is studied.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2018. , p. 85
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2018:01
Keywords [en]
Theoretical spectroscopy, cubic response theory, damped response theory, magnetic circular dichroism, linear birefringence, two-photon absorption, TPA, resonant-inelastic x-ray scattering, RIXS, DALTON program
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
URN: urn:nbn:se:kth:diva-218662ISBN: 978-91-7729-627-0 (print)OAI: oai:DiVA.org:kth-218662DiVA, id: diva2:1161279
Public defence
2018-02-28, FA32, Roslagstullsbacken 21, Albanova, Stockholm, 10:00 (English)
Opponent
Supervisors
Funder
Knut and Alice Wallenberg Foundation, KAW- 2013.0020Swedish Research Council, 621-2014-4646
Note

QC 20180108

Available from: 2018-01-08 Created: 2017-11-29 Last updated: 2018-01-08Bibliographically approved
List of papers
1. A Polarization Propagator for Nonlinear X-ray Spectroscopies
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
American Chemical Society, 2016
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-189373 (URN)10.1021/acs.jpclett.6b00750 (DOI)000377239200009 ()27159130 (PubMedID)2-s2.0-84973568630 (Scopus ID)
Note

QC 20160707

Available from: 2016-07-07 Created: 2016-07-04 Last updated: 2017-11-29Bibliographically approved
2. Resonant-convergent second-order nonlinear response functions at the levels of Hartree-Fock and Kohn-Sham density functional theory
Open this publication in new window or tab >>Resonant-convergent second-order nonlinear response functions at the levels of Hartree-Fock and Kohn-Sham density functional theory
2017 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, no 14, article id 144109Article in journal (Refereed) Published
Abstract [en]

The second-order nonlinear (or cubic) response function is derived from the Ehrenfest theorem with inclusion made of the finite lifetimes of the excited states, representing the extension of the derivation of the quadratic response function in the same framework [P. Norman et al., J. Chem. Phys. 123, 194103 (2005)]. The resulting damped response functions are physically sound and converging also in near-resonance and resonance regions of the spectrum. Being an accurate approximation for small complex frequencies (defined as the sum of an optical frequency and an imaginary damping parameter), the polynomial expansion of the complex cubic response function in terms of the said frequencies is presented and used to validate the program implementation. In terms of approximate state theory, the computationally tractable expressions of the damped cubic response function are derived and implemented at the levels of Hartree-Fock and Kohn-Sham density functional theory. Numerical examples are provided in terms of studies of the intensity-dependent refractive index of para-nitroaniline and the two-photon absorption cross section of neon. For the latter property, a numerical comparison is made against calculations of the square of two-photon matrix elements that are identified from a residue analysis of the resonance-divergent quadratic response function.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2017
National Category
Theoretical Chemistry Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-217190 (URN)10.1063/1.4991616 (DOI)000413201100012 ()29031277 (PubMedID)2-s2.0-85031678376 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish Research Council, 621-2014-4646
Note

QC 20171103

Available from: 2017-11-03 Created: 2017-11-03 Last updated: 2017-11-29Bibliographically approved
3. A density functional theory study of magneto-electric Jones birefringence of noble gases, furan homologues, and mono-substituted benzenes
Open this publication in new window or tab >>A density functional theory study of magneto-electric Jones birefringence of noble gases, furan homologues, and mono-substituted benzenes
Show others...
2013 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, no 19, article id 194311Article in journal (Refereed) Published
Abstract [en]

We report on the results of a systematic ab initio study of the Jones birefringence of noble gases, of furan homologues, and of monosubstituted benzenes, in the gas phase, with the aim of analyzing the behavior and the trends within a list of systems of varying size and complexity, and of identifying candidates for a combined experimental/theoretical study of the effect. We resort here to analytic linear and nonlinear response functions in the framework of time-dependent density functional theory. A correlation is made between the observable (the Jones constant) and the atomic radius for noble gases, or the permanent electric dipole and a structure/chemical reactivity descriptor as the para Hammett constant for substituted benzenes. © 2013 AIP Publishing LLC.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2013
Keywords
Density functional theory studies, Electric dipole, Hammett constants, Monosubstituted benzenes, Non-linear response, Reactivity descriptor, Substituted benzenes, Time dependent density functional theory, Aromatic compounds, Benzene, Birefringence, Density functional theory, Organic pollutants, Inert gases, benzene derivative, furan, furan derivative, inert gas, article, chemistry, electromagnetic field, quantum theory, Benzene Derivatives, Electromagnetic Fields, Furans, Noble Gases
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-198732 (URN)10.1063/1.4830412 (DOI)000327714900024 ()2-s2.0-84903366467 (Scopus ID)
Note

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Available from: 2016-12-22 Created: 2016-12-21 Last updated: 2017-11-29Bibliographically approved
4. A QM/MM and QM/QM/MM study of Kerr, Cotton--Mouton and Jones linear birefringences in liquid acetonitrile
Open this publication in new window or tab >>A QM/MM and QM/QM/MM study of Kerr, Cotton--Mouton and Jones linear birefringences in liquid acetonitrile
2017 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal, Editorial material (Refereed) Submitted
Abstract [en]

QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear bire-fringences Kerr, Cotton–Mouton, and Jones, as shown by acetonitrile in the gas and pureliquid phases. The relevant first-order properties as well as linear, quadratic, and cubicfrequency-dependent response functions were computed using time-dependent Kohn–Shamdensity-functional theory with use of the standard CAM-B3LYP functional. In the liquid phase,a series of room temperature (293.15 K) molecular dynamics snapshots were selected, for whichaveraged values of the observables were obtained at an optical wavelength of 632.8 nm. Thebirefringences were computed for electric and magnetic induction fields corresponding to the lab-oratory setup previously employed by Roth and Rikken in Phys. Rev. Lett. 85, 4478, (2000).Under these conditions, acetonitrile is shown to exhibit a weak Jones response — in fact roughly6.5 times smaller than the limit of detection of the apparatus employed in the measurementsmentioned above. A comparison is made with the corresponding gas-phase results and an as-sessment is made of the index of measureability, estimating the degree of overlap of the threebirefringences in actual measurements. For acetonitrile, it is shown that this index is a factorof 3.6 and 6.7 larger than that of methylcyclopentadienyl-Mn-tricarbonyl and cyclohexadienyl-Fe-tricarbonyl, respectively — two compounds reported in Phys. Rev. Lett. 85, 4478, (2000) to exhibita strong Jones signal.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017
Keywords
Linear birefringence, Jones, Kerr, Cotton--Mouton, QM/MM, QM/QM/MM, PE, PDE
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology; Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-218665 (URN)
Funder
Swedish Research Council
Note

QC 20171211

Available from: 2017-11-29 Created: 2017-11-29 Last updated: 2017-12-11Bibliographically approved
5. The magnetic circular dichroism spectrum of the C 60 fullerene
Open this publication in new window or tab >>The magnetic circular dichroism spectrum of the C 60 fullerene
2013 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, no 9-11, p. 1401-1404Article in journal (Refereed) Published
Abstract [en]

The magnetic circular dichroism spectrum of the C60 fullerene has been determined with the use of Kohn-Sham density functional theory in conjunction with the CAM-B3LYP exchange-correlation functional. The experimental spectrum of Gasyna et al. [Chem. Phys. Lett. 183, 283 (1991)] covering the wavelength region above 200 nm is explained by the signal responses from the three lowest singlet states of T 1u symmetry. © 2013 Copyright Taylor and Francis Group, LLC.

Place, publisher, year, edition, pages
Taylor & Francis, 2013
Keywords
C60, density functional theory, DFT, fullerene, magnetic circular dichroism, MCD, response theory, Magnetic circular dichroisms, Fullerenes, Spectroscopy
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-198735 (URN)10.1080/00268976.2013.779394 (DOI)000323409600035 ()2-s2.0-84882455394 (Scopus ID)
Note

References: Sattler, K.D., (2010) Handbook of Nanophysics: Clusters and Fullerenes, , Cambridge: Cambridge University Press; Sassara, A., Zerza, G., Chergui, M., Negri, F., Orlandi, G., (1997) J. Chem. Phys., 107, p. 8731; Marconi, G., Salvi, P.R., (1993) Chem. Phys. Lett., 202, p. 335; Yagi, H., Nakajima, K., Koswattage, K.R., Nakagawa, K., Huang, C., Prodhan, M.S.I., Kafle, B.P., Mitsuke, K., (2009) Carbon, 47, p. 1152; Kawashita, Y., Yabana, K., Noda, M., Nobusada, K., Nakatsukasa, T., (2009) J. Mol. Struct.: THEOCHEM, 914, p. 130; Bishop, D.M., (1998) Adv. Chem. Phys., 104, p. 1; Barron, L.D., (2004) Molecular Light Scattering and Optical Activity, , 2nd, Cambridge: Cambridge University Press; Norman, P., Bishop, D.M., Jensen, H.J.A., Oddershede, J., (2005) J. Chem. Phys., 123, p. 194103; Solheim, H., Ruud, K., Coriani, S., Norman, P., (2008) J. Chem. Phys., 128, p. 094103; Solheim, H., Ruud, K., Coriani, S., Norman, P., (2008) J. Phys. Chem.,A, 112, p. 9615; Kauczor, J., Jørgensen, P., Norman, P., (2011) J. Chem. Theory Comput., 7, p. 1610; Becke, A.D., (1993) J. Chem. Phys., 98, p. 5648; Yanai, T., Tew, D.P., Handy, N.C., (2004) Chem. Phys. Lett., 393, p. 51; Sadlej, A., (1988) Collect. Czech. Chem. Commun., 53, p. 1995; (2011) DALTON. 2011. A Molecular Electronic Structure Program, Release Dalton, , see http://daltonprogram.org/; Dunning, T.H., (1989) J. Chem. Phys., 90, p. 1007; Gasyna, Z., Schatz, P.N., Hare, J.P., Dennis, T.J., Kroto, H.W., Taylor, R., Walton, D.R.M., (1991) Chem. Phys. Lett., 183, p. 283; Pilch, M., Pawlikowski, M., Mortensen, O.S., (1993) Chem. Phys., 172, p. 277; Lee, K.M., Yabana, K., Bertsch, G.F., (2011) J. Chem. Phys., 134, p. 144106; Paterson, M.J., Christiansen, O., Pawłowski, F., Jørgensen, P., Hättig, C., Helgaker, T., Sałek, P., (2006) J. Chem. Phys., 124, p. 054322. QC 20170111

Available from: 2016-12-22 Created: 2016-12-21 Last updated: 2017-11-29Bibliographically approved
6. Relative stability of the La and Lb excited states in adenine and guanine: Direct evidence from TD-DFT calculations of MCD spectra
Open this publication in new window or tab >>Relative stability of the La and Lb excited states in adenine and guanine: Direct evidence from TD-DFT calculations of MCD spectra
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2014 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 5, no 11, p. 1806-1811Article in journal (Refereed) Published
Abstract [en]

The relative position of La and Lb ππ* electronic states in purine nucleobases is a much debated topic, since it can strongly affect our understanding of their photoexcited dynamics. To assess this point, we calculated the absorption and magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides in gas-phase and aqueous solution, exploiting recent developments in MCD computational technology within time-dependent density functional theory. MCD spectroscopy allows us to resolve the intense S0 La transition from the weak S 0Lb transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP functionals and describing solvent effect by cluster models and by the polarizable continuum model (PCM), are in very good agreement with the experimental counterparts, thus providing direct and unambiguous evidence that the energy ordering predicted by TD-DFT, La < L b, is the correct one.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2014
Keywords
complex polarization propagator, DNA bases, hidden transitions, magnetic circular dichroism, photostability, solvent effect, Continuum mechanics, Density functional theory, Solvents, Spectroscopy, DNA basis, Magnetic circular dichroisms, Photo-stability, Solvent effects, Positive ions
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-198721 (URN)10.1021/jz500633t (DOI)000337012500005 ()26273857 (PubMedID)2-s2.0-84902075875 (Scopus ID)
Note

QC 20161222

Available from: 2016-12-22 Created: 2016-12-21 Last updated: 2017-11-29Bibliographically approved
7. TD-DFT investigation of the magnetic circular dichroism spectra of some purine and pyrimidine bases of nucleic acids
Open this publication in new window or tab >>TD-DFT investigation of the magnetic circular dichroism spectra of some purine and pyrimidine bases of nucleic acids
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2015 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5476-5489Article in journal (Refereed) Published
Abstract [en]

We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright π → π∗ transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π∗ excitations, but they are too weak to be observed in the experiment. © 2015 American Chemical Society.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2015
Keywords
Aromatic compounds, Biomolecules, Continuum mechanics, Molecules, Nucleic acids, Solvents, Spectroscopy, Computational studies, Energy differences, Explicit water molecules, Magnetic circular dichroism spectra, Magnetic circular dichroisms, Polarizable continuum model, Qualitative shapes, Wavelength regions, Dichroism, cytosine, gas, solvent, thymine, uracil, water, chemical model, chemistry, circular dichroism, computer simulation, Gases, Models, Chemical
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-198714 (URN)10.1021/jp512468k (DOI)000355495100043 ()2-s2.0-84930634429 (Scopus ID)
Note

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Lett., 5, pp. 1806-1811; Szalay, P., Watson, T., Perera, A., Lotrich, V., Bartlett, R., Benchmark Studies on the Building Blocks of DNA. 1. Superiority of Coupled Cluster Methods in Describing the Excited States of Nucleobases in the Franck-Condon Region (2012) J. Phys. Chem. A, 116, pp. 6702-6710; Hare, P.M., Crespo-Hernández, C.E., Kohler, B., Internal Conversion to the Electronic Ground State Occurs via Two Distinct Pathways for Pyrimidine Bases in Aqueous Solution (2007) Proc. Natl. Acad. Sci. U. S. A., 104, pp. 435-440; Santoro, F., Barone, V., Gustavsson, T., Improta, R., Solvent Effect on the Singlet Excited-State Lifetimes of Nucleic Acid Bases: A Computational Study of 5-Fluorouracil and Uracil in Acetonitrile and Water (2006) J. Am. Chem. Soc., 128, pp. 16312-16322; Improta, R., Barone, V., Lami, A., Santoro, F., Quantum Dynamics of the Ultrafast ππ/nπ∗ Population Transfer in Uracil and 5-Fluoro-Uracil in Water and Acetonitrile (2009) J. Phys. Chem. 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Phys., 119, pp. 5818-5827; Frediani, L., Ågren, H., Ferrighi, L., Ruud, K., Second-Harmonic Generation of Solvated Molecules Using Multiconfigurational Self-Consistent-Field Quadratic Response Theory and the Polarizable Continuum Model (2005) J. Chem. Phys., 123, p. 144117; Milne, B.F., Norman, P., Resonant-Convergent PCM Response Theory Calculations of Second Harmonic Generation in Makaluvamines A-V; Pyrroloiminoquinone Marine Natural Products from Poriferans of Genus Zyzzya (2015) J. Phys. Chem. A; Improta, R., Barone, V., Absorption and Fluorescence Spectra of Uracil in the Gas Phase and in Aqueous Solution: A TD-DFT Quantum Mechanical Study (2004) J. Am. Chem. Soc., 126, pp. 14320-21432; Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Petersson, G.A., (2009) Gaussian 09, , Revision C.3; Gaussian Inc. 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Available from: 2016-12-22 Created: 2016-12-21 Last updated: 2017-11-29Bibliographically approved
8. Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution
Open this publication in new window or tab >>Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution
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2017 (English)In: Photochemical and Photobiological Sciences, ISSN 1474-905X, E-ISSN 1474-9092, Vol. 16, no 9, p. 1415-1423Article in journal (Refereed) Published
Abstract [en]

The excited electronic states of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the time-dependent density functional theory level. Special attention has been paid to solvent effects, included by a mixed discrete/continuum model, and to determining how our results depend on the adopted DFT functional (CAM-B3LYP and B3LYP). Whereas including solvent effects does not dramatically impact the MCD and OPA spectra, though improving the agreement with the experimental spectra, the performances of CAM-B3LYP and B3LYP are remarkably different. CAM-B3LYP captures well the effect of thionation on the uracil excited states and provides spectra in good agreement with the experiments, whereas B3LYP shows some deficiency in describing 2-TU and 2,4-DTU spectra, despite being more accurate than CAM-B3LYP for 4-TU.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-215374 (URN)10.1039/c7pp00105c (DOI)000410665500008 ()28745752 (PubMedID)2-s2.0-85029509510 (Scopus ID)
Funder
Swedish Research Council, 621-2014-4646
Note

QC 20171009

Available from: 2017-10-09 Created: 2017-10-09 Last updated: 2017-11-29Bibliographically approved

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