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• 1.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Bicarbonate hydrogenation by iron: Effects of solvent and ligand on the mechanism2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
• 2.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Modeling molecular water oxidation catalysts at interfaces2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
• 3.
KTH, School of Engineering Sciences (SCI), Applied Physics. Photonics Laboratory, Physics Department, Kharazmi University, Tehran, Iran.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics. Centre for Optical and Electromagnetic Research, Guangdong Provincial Key Laboratory of Optical Information. Centre for Optical and Electromagnetic Research, Guangdong Provincial Key Laboratory of Optical Information. Photonics Laboratory, Physics Department, Kharazmi University, Tehran, Iran. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
Change in the emission saturation and kinetics of upconversion nanoparticles under different light irradiations2019In: Optical materials (Amsterdam), ISSN 0925-3467, E-ISSN 1873-1252, Vol. 97, article id 109389Article in journal (Refereed)

Nd3+-sensitized upconversion nanoparticles (UCNPs) can be excited by both 980 and 808 nm light, which is regarded as a particularly advantageous property of these particles. In this work, we demonstrate that the nanoparticles can exhibit significantly different response when excited at these two excitation wavelengths, showing dependence on the intensity of the excitation light and the way it is distributed in time. Specifically, with 808 nm excitation saturation in the emitted luminescence is more readily reached with increasing excitation intensities than upon 980 nm excitation. This is accompanied by delayed upconversion luminescence (UCL) kinetics and weaker UCL intensities. The different luminescence response at 808 and 980 nm excitation reported in this work is relevant in a manifold of applications using UCNPs as labels and sensors. This could also open new possibilities for multi-wavelength excitable UCNPs for upconversion color display and in laser-scanning microscopy providing selective readouts and sub-sectioning of samples.

• 4.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia..
Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia.. Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
Vibronic absorption spectra of the angular fused bisindolo- and biscarbazoloanthracene blue fluorophores for OLED applications2018In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 513, p. 105-111Article in journal (Refereed)

An in-depth analysis of the vibronic absorption spectra for the recently synthesized blue-fluorescent OLED emitters bis[(1,2)(5,6)]indoloanthracene and biscarbazolo[3,4-a:3',4'-h]anthracene has been carried out computationally at the density functional theory level within the Franck-Condon approximation. These molecules are characterized by extended and rich electronic absorption spectra with most absorption bands being of vibronic origin. The first excited singlet state of bis[(1,2)(5,6)]indoloanthracene compound demonstrates a clear observable double-peak vibronic progression for two different active modes in the absorption spectrum, while the S-2 state is vibronically inactive. In contrast, for the larger biscarbazolo[3,4-a:3',4'-h]anthracene compound the S-0 -> S-2 transition demonstrates well-resolved intense vibronic bands which overlap the less intense progressions of few modes in the S-0 -> S-1 transition. We have also found, that even the higher-lying and very intense S-0 -> S-4 and S-0 -> S-5 transitions for bis[(1,2)(5,6)]indoloanthracene and biscarbazolo[3,4-a:3',4'-h]anthracene, respectively, are characterized by clear vibronic progressions in excellent agreement with experimental spectra.

• 5.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Dept Chem, FIN-00014 Helsinki, Finland.. Tomsk State Univ, 36 Lenin Ave, Tomsk, Russia.. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Aromaticity and photophysics of tetrasila- and tetragerma-annelated tetrathienylenes as new representatives of the hetero[8]circulene family2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 18, p. 9246-9254Article in journal (Refereed)

The electronic structure, absorption and emission spectra, aromaticity and photophysical behavior of the recently synthesized tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene compounds have been studied computationally. Both compounds demonstrate a specific bifacial aromaticity, which is unusual for hetero[8]circulenes; the inner eight-membered core sustains an expected strong paratropic magnetically-induced ring current, while the outer perimeter contains saturated Si(Et)(2) and Ge(Et)(2) moieties which break the conjugation between the thiophene rings. The overall magnetically-induced ring current for both studied circulenes is close to zero because of the strong local diatropic currents in each thiophene ring that compensate the paratropic counterpart. The electronic absorption and emission spectra of tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene demonstrate a clear visible vibronic progression. The 0-0 band is the most active one in the absorption spectra, while in the fluorescence spectra the 0-1 band composed of several normal vibrations is more intense compared with the 0-0 band in excellent agreement with experiment. Accounting for spin-orbit coupling effects, an analysis of the photophysical constants for the two compounds demonstrates: (1) a clear manifestation of the internal heavy atom effect on the inter-system crossing efficiency; (2) one to two order domination of non-radiative rates over the fluorescence rate; and (3) that the S-1-S-0 internal conversion is extremely slow and can not compete with the fluorescence, while the S-1-T-n inter-system crossing is a main deactivation channel of the S-1 excited state. These results provide new insight into the electronic structure and photophysics of tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene as novel standalone representatives of hetero[8]circulenes - tetraannelated derivatives of tetrathienylene.

• 6.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.
Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Fac Sci, Dept Chem, FIN-00014 Helsinki, Finland.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Div Theoret Phys & Wave Phenomena, 79 Svobodniy Av, Krasnoyarsk 660041, Russia. Univ Helsinki, Fac Sci, Dept Chem, FIN-00014 Helsinki, Finland.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.
Cyclo[18]carbon: Insight into Electronic Structure, Aromaticity, and Surface Coupling2019In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 21, p. 6701-6705Article in journal (Refereed)

Cyclo[18]carbon (C-18) is studied computationally at the density functional theory (DFT) and ab initio levels to obtain insight into its electronic structure, aromaticity, and adsorption properties on a NaCl surface. DFT functionals with a small amount of Hartree-Fock exchange fail to determine the experimentally observed polyyne molecular structure, revealing a cumulene-type geometry. Exchange-correlation functionals with a large amount of Hartree-Fock exchange as well as ab initio CASSCF calculations yield the polyyne structure as the ground state and the cumulene structure as a transition state between the two inverted polyyne structures through a Kekule distortion. The polyyne and the cumulene structures are found to be doubly Huckel aromatic. The calculated adsorption energy of cyclo[18]carbon on the NaCl surface is small (37 meV/C) and almost the same for both structures, implying that the surface does not stabilize a particular geometry.

• 7.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Dept Chem, FIN-00014 Helsinki, Finland.. East China Univ Sci & Technol, Sch Chem & Mol Engn, Key Lab Adv Mat & Joint Int Res Lab Precis Chem &, Shanghai 200237, Peoples R China.. East China Univ Sci & Technol, Sch Chem & Mol Engn, Key Lab Adv Mat & Joint Int Res Lab Precis Chem &, Shanghai 200237, Peoples R China.. East China Univ Sci & Technol, Sch Chem & Mol Engn, Key Lab Adv Mat & Joint Int Res Lab Precis Chem &, Shanghai 200237, Peoples R China.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Computational study of aromaticity, H-1 NMR spectra and intermolecular interactions of twisted thia-norhexaphyrin and its multiply annulated polypyrrolic derivatives2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 45, p. 25334-25343Article in journal (Refereed)

The recently synthesized twisted thia-norhexaphyrin and its multiply annulated polypyrrolic derivatives have been studied computationally. Gauge-including magnetically induced current calculations predict a global nonaromatic character of the initial thia-norhexaphyrin due to the highly-twisted conformation of the macrocycle. Upon the oxidation of the thia-norhexaphyrin four multiply annulated polypyrrolic aromatic macrocycles are formed for which the global aromatic character is confirmed in agreement with experimentally measured H-1 NMR spectra. The calculation of the proton chemical shifts for the studied compounds by direct comparison with the tetramethylsilane standard leads to a significant mean absolute error. At the same time a linear regression procedure for the two selected groups of protons (CH and NH protons) provides much better values of calculated chemical shifts and tight correlation with experiment. The separate consideration of NH protons is motivated by the numerous intermolecular hydrogen bonds in which the protons are involved, which induce considerable upfield shifts, leading to a significant underestimation of the corresponding chemical shifts. Such a selected correlation can be used for accurate estimation of proton chemical shifts of the related porphyrinoids. Bader's theory of Atoms in Molecules has been applied for the studied twisted thia-norhexaphyrin and its multiply annulated polypyrrolic derivatives to characterize intramolecular H-bonds and other non-covalent interactions.

• 8. Baryshnikova, A. T.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Computational study of the structure and magnetic properties of the weakly-coupled tetranuclear square-planar complex of Cu(II) with a tetraporphyrin sheet2019In: Inorganica Chimica Acta, ISSN 0020-1693, E-ISSN 1873-3255, Vol. 485, p. 73-79Article in journal (Refereed)

Owing to the fact that weakly-coupled Cu(II) complexes are potentially applicable in the fields of spintronics and single-molecule magnets we have studied one particularly conspicuous case – a tetranuclear square-planar complex of Cu(II) ions with a π-extended tetraporphyrin ligand (Tetrahedron, 2008, 64, 11433), the structural criteria of which, with very long distances between the paramagnetic centers, can sensibly define the exchange coupling constants and magnetic behaviour. We use the “broken symmetry” density functional theory formalism for various spin states (open-shell singlet, triplet and quintet states). The calculated value of the magnetic exchange integral corresponds to a very weak antiferromagnetic coupling between the neighboring Cu(II) ions (Jcalc = –1.48 cm−1(calculated) Jexp = −1.16 cm−1 (experiment)). The opposite Cu(II) ions are coupled ferromagnetically with an extremely small exchange constant (jcalc = 0.09 cm−1 (calculated) that corresponds to the open-shell singlet ground state of the following spin configuration↑↓↑↓. The exchange mechanism between the [Cu(n) + 4N] localized singly-occupied “magnetic” orbitals of the dxy(Cu) + 4sp2(N) nature indicates a diffuse non-zero overlap between them on the Carbon atoms of the organic ligand. The numerical analysis of atomic spin densities and corresponding decomposition coefficients for the singly-occupied “magnetic” orbitals confirm the proposed exchange mechanism. This superexchange pathway is mediated by the in-plane sp2-hybrid orbitals of the Carbon atoms that couple four [Cu + 4N] fragments by the σ-bond system. For more detailed characterization of the target system a topological analysis of electron density distributions in the high-spin quintet states has been carried out using the Bader's method “quantum theory of atoms in molecules”.

• 9.
Siberian Fed Univ, 79 Svobodny Av, Krasnoyarsk 660041, Russia..
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, 79 Svobodny Av, Krasnoyarsk 660041, Russia.;Kirensky Inst Phys SB RAS, 50-38 Akademgorodok, Krasnoyarsk 660036, Russia.. Siberian Fed Univ, 79 Svobodny Av, Krasnoyarsk 660041, Russia.;Kirensky Inst Phys SB RAS, 50-38 Akademgorodok, Krasnoyarsk 660036, Russia.. Siberian Fed Univ, 79 Svobodny Av, Krasnoyarsk 660041, Russia.;Kirensky Inst Phys SB RAS, 50-38 Akademgorodok, Krasnoyarsk 660036, Russia.. Siberian Fed Univ, 79 Svobodny Av, Krasnoyarsk 660041, Russia.. Kyungpook Natl Univ, Dept Chem, 80 Daehakro, Daegu 41566, South Korea..
Triple VTe2/graphene/VTe2 heterostructures as perspective magnetic tunnel junctions2020In: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 510, article id 145315Article in journal (Refereed)

New perspective 1.4 nm thick spin-polarized triple heterostructures based on graphene sandwiched between two vanadium ditelluride monolayers (VTe2/graphene/VTe2) were studied using ab initio DFT technique. Both possible trigonal prismatic (H-VTe2) and octahedral (T-VTe2) VTe2 phases were considered to design and study graphene-based heterostructures. It was shown that the interaction with graphene changes the electronic structure of 2D T-VTe2 from metallic to half-metallic, making T phase perspective to be used for magnetic tunnel junctions. The electronic subsystem of graphene fragment is slightly hole doped. Calculated tunnel magne-toresistance ratio for the favorable heterostructure configuration estimated within the Julliere model is 220%, which opens a way to use VTe2/graphene/VTe2 as prospective magnetic tunnel junction in novel spintronic nanodevices based on tunnel magnetic resistance and spin transfer torque effects.

• 10.
KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
On the decay time of upconversion luminescence2019In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 11, no 11, p. 4959-4969Article in journal (Refereed)

In this study, we systematically investigate the decay characteristics of upconversion luminescence (UCL) under anti-Stokes excitation through numerical simulations based on rate-equation models. We find that a UCL decay profile generally involves contributions from the sensitizer's excited-state lifetime, energy transfer and cross-relaxation processes. It should thus be regarded as the overall temporal response of the whole upconversion system to the excitation function rather than the intrinsic lifetime of the luminescence emitting state. Only under certain conditions, such as when the effective lifetime of the sensitizer's excited state is significantly shorter than that of the UCL emitting state and of the absence of cross-relaxation processes involving the emitting energy level, the UCL decay time approaches the intrinsic lifetime of the emitting state. Subsequently, Stokes excitation is generally preferred in order to accurately quantify the intrinsic lifetime of the emitting state. However, possible cross-relaxation between doped ions at high doping levels can complicate the decay characteristics of the luminescence and even make the Stokes-excitation approach fail. A strong cross-relaxation process can also account for the power dependence of the decay characteristics of UCL.

• 11.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Korea Adv Inst Sci & Technol, Dept Chem, Daejeon 34141, South Korea..
Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.;Orebro Univ, Sch Sci & Technol, S-70182 Orebro, Sweden.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Photoelectron Spectroscopy of Molecules Beyond the Electric Dipole Approximation2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 10, p. 5483-5494Article in journal (Refereed)

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.

• 12.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Korea Adv Inst Sci & Technol, Dept Chem, Daejeon 34141, South Korea..
Uppsala Univ, Dept Phys & Astron, SE-75120 Uppsala, Sweden.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Atomic photoionization cross sections beyond the electric dipole approximation2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 4, article id 044306Article in journal (Refereed)

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).

• 13.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.. Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.. Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.. Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
Ligand Effects on the Linear Response Hubbard U: The Case of Transition Metal Phthalocyanines2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 14, p. 3214-3222Article in journal (Refereed)

It is established that density functional theory (DFT) + U is a better choice compared to DFT for describing the correlated electron metal center in organometallics. The value of the Hubbard U parameter may be determined from linear response, either by considering the response of the metal site alone or by additionally considering the response of other sites in the compound. We analyze here in detail the influence of ligand shells of increasing size on the U parameter calculated from the linear response for five transition metal phthalocyanines. We show that the calculated multiple-site U ligand atoms that are mainly responsible for this difference are is larger than the single-site U by as much as 1 eV and the ligand atoms that are mainly responsible for this difference are the isoindole nitrogen atoms directly bonded to the central metal atom. This suggests that a different U value may be required for computations of chemisorbed molecules compared to physisorbed and gas-phase cases.

• 14. Carravetta, V.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
PH-dependent X-ray Photoelectron Chemical Shifts and Surface Distribution of Cysteine in Aqueous Solution2019In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 17, p. 3776-3785Article in journal (Refereed)

The distribution and protonation states of amino acids in water droplets are of considerable concern in studies on the formation of clouds in the atmosphere as well as in many biological contexts. In the present work we use the amino acid cysteine as a prototypical example and explore the protonation states of this molecule in aqueous solution, which are strongly affected by the acidity of the environment and also can show different distributions between surface and bulk. We use a combination of X-ray photoelectron chemical shift measurements, density functional theory calculations of the shifts, and reactive force field molecular dynamics simulations of the underlying structural dynamics. We explore how the photoelectron spectra distinctly reflect the different protonation states that are generated by variation of the solution acidity and how the distribution of these protonation states can differ between bulk and surface regions. At specific pH values, we find that the distribution of the cysteine species at the surface is quite different from that in bulk, in particular, for the appearance in the surface region of species which do not exist in bulk. Some ramifications of this finding are discussed.

• 15.
Synchrotron SOLEIL, F-91191 Gif Sur Yvette, France..
North China Elect Power Univ, Dept Math & Phys, Beijing 102206, Peoples R China.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.. Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France.. Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France.. Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France.. Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France.. Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.;Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France.. Free Univ Berlin, Fachbereich Phys, D-14195 Berlin, Germany.. Sorbonne Univ, CNRS, LCPMR, F-75005 Paris, France.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Synchrotron SOLEIL, F-91191 Gif Sur Yvette, France.;Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effect2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 11, p. 4877-4882Article in journal (Refereed)

Observing and controlling molecular motion and in particular rotation are fundamental topics in physics and chemistry. To initiate ultrafast rotation, one needs a way to transfer a large angular momentum to the molecule. As a showcase, this was performed by hard X-ray C1s ionization of carbon monoxide accompanied by spinning up the molecule via the recoil "kick" of the emitted fast photoelectron. To visualize this molecular motion, we use the dynamical rotational Doppler effect and an X-ray "pump-probe" device offered by nature itself: the recoil-induced ultrafast rotation is probed by subsequent Auger electron emission. The time information in our experiment originates from the natural delay between the C1s photoionization initiating the rotation and the ejection of the Auger electron. From a more general point of view, time-resolved measurements can be performed in two ways: either to vary the "delay" time as in conventional time-resolved pump-probe spectroscopy and use the dynamics given by the system, or to keep constant delay time and manipulate the dynamics. Since in our experiment we cannot change the delay time given by the core-hole lifetime tau, we use the second option and control the rotational speed by changing the kinetic energy of the photoelectron. The recoil-induced rotational dynamics controlled in such a way is observed as a photon energy-dependent asymmetry of the Auger line shape, in full agreement with theory. This asymmetry is explained by a significant change of the molecular orientation during the core-hole lifetime, which is comparable with the rotational period.

• 16. Chen, J.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Allosteric inhibitor remotely modulates the conformation of the orthestric pockets in mutant IDH2/R140Q2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, no 1, article id 16458Article in journal (Refereed)

Neomorphic mutation R140Q in the metabolic enzyme isocitrate dehydrogenase 2 (IDH2) is found to be a driver mutation in cancers. Recent studies revealed that allosteric inhibitors could selectively inhibit IDH2/R140Q and induce differentiation of TF-1 erythroleukemia and primary human AML cells. However, the allosteric inhibition mechanism is not very clear. Here, we report the results from computational studies that AGI-6780 binds tightly with the divalent cation binding helices at the homodimer interface and prevents the transition of IDH2/R140Q homodimer to a closed conformation that is required for catalysis, resulting in the decrease of the binding free energy of NADPHs. If the allosteric inhibitor is removed, the original open catalytic center of IDH2/R140Q will gradually reorganize to a quasi-closed conformation and the enzymatic activity might recover. Unlike IDH2/R140Q, AGI-6780 locks one monomer of the wild-type IDH2 in an inactive open conformation and the other in a half-closed conformation, which can be used to explain the selectivity of AGI-6780. Our results suggest that conformational changes are the primary contributors to the inhibitory potency of the allosteric inhibitor. Our study will also facilitate the understanding of the inhibitory and selective mechanisms of AG-221 (a promising allosteric inhibitor that has been approved by FDA) for mutant IDH2.

• 17.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden University, Leiden Observatory, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands.
Formation of Covalently Bonded Polycyclic Aromatic Hydrocarbons in the Interstellar Medium2018In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 866, no 113Article in journal (Refereed)

Photo-/ion-induced ionization and dissociation processes are commonly observed for polycyclic aromatic hydrocarbon (PAH) molecules. This work performs theoretical studies of PAHs and their fragments. Molecular dynamics simulations in combination with static quantum chemical calculations reveal that following a single hydrogen atom loss, the fragments, PAH-H, are extremely reactive. They catch a neighbor molecule within picoseconds to form a covalently bonded large molecule regardless of orientations/angles and temperatures. We calculate the infrared spectra of the covalently bonded molecules, which indicate that such species could be the carrier of unidentified infrared emission bands. It also implies that regular PAHs might be less abundant in space than what is expected.

• 18.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Temperature effects on anharmonic infrared spectra of large compact polycyclic aromatic hydrocarbons2019In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 622, article id A152Article in journal (Refereed)

Aims. Large compact polycyclic aromatic hydrocarbon molecules (PAHs) present special interest in the astrochemical community. A key issue in analyses of large PAHs is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the infrared (IR) spectra for molecules under various conditions. Methods. Because of the huge amount of interactions/resonances in large PAHs, no anharmonic IR spectrum can be produced with static/time-independent ab initio method, especially for the molecules with D6h symmetry, e.g., coronene and circumcoronene. In this work, we performed molecular dynamics simulations to generate anharmonic IR spectra of coronene and circumcoronene. Results. The method is validated for small PAHs, i.e., naphthalene and pyrene. We find that the semiempirical method PM3 produces accurate band positions with an error <5 cm(-1). Furthermore, we calculate the spectra at multiple temperatures and find a clear trend toward band shifting and broadening.

• 19.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands.
The Carrier of 3.3 mu m Aromatic Infrared Bands: Anharmonicity and Temperature Effects on Neutral PAHs2018In: Astrophysical Journal Supplement Series, ISSN 0067-0049, E-ISSN 1538-4365, Vol. 238, no 2, article id 18Article in journal (Refereed)

Anharmonic infrared (IR) spectra are crucial for the study of interstellar polycyclic aromatic hydrocarbon (PAH) molecules. This work aims to provide a comprehensive study of the features that may influence the accuracy of anharmonic IR spectra of PAHs so that a reliable spectrum that incorporates all necessary features for interpreting the observational IR spectra can be obtained. Six PAHs are investigated: naphthalene, anthracene, pyrene, chrysene, 9,10-dimethylanthracene, and 9,10-dihydroanthracene. The NIST spectra and high-resolution IR absorption spectra are utilized as the reference for the comparisons. The influences of different resonances and resonant thresholds are studied. Four methods for electronic structure calculations are tested. The quantitative comparisons indicate that for the NIST data, B3LYP/NO7D provides the best agreement with measured spectra concerning band positions and B3LYP/cc-pVTZ is superior in the description of the relative intensities. The importance of 1-3 Darling-Dennison resonances, which are required for generating triple combination bands, is investigated through a comparison to a high-resolution experimental spectrum. For interpreting the bandwidths and profiles of the observational spectra, the temperature effects are included through the Wand-Landau random walk technique. The comparisons between calculated high-temperature anharmonic and observational spectra indicate that small and compact PAHs might be responsible for the 3.3 mu m aromatic infrared bands.

• 20.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Univ Missouri, Dept Phys & Astron, Columbia, MO 65211 USA..
Synthesizing carbon nanotubes in space2019In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 631, article id A54Article in journal (Refereed)

Context. As the fourth most abundant element in the universe, carbon (C) is widespread in the interstellar medium (ISM) in various allotropic forms (e.g. fullerenes have been identified unambiguously in many astronomical environments, the presence of polycyclic aromatic hydrocarbon molecules in space has been commonly acknowledged, and presolar graphite, as well as nanodiamonds, have been identified in meteorites). As stable allotropes of these species, whether carbon nanotubes (CNTs) and their hydrogenated counterparts are also present in the ISM or not is unknown. Aims. The aim of the present works is to explore the possible routes for the formation of CNTs in the ISM and calculate their fingerprint vibrational spectral features in the infrared (IR). Methods. We studied the hydrogen-abstraction and acetylene-addition (HACA) mechanism and investigated the synthesis of nanotubes using density functional theory (DFT). The IR vibrational spectra of CNTs and hydrogenated nanotubes (HNTs), as well as their cations, were obtained with DFT. Results. We find that CNTs could be synthesized in space through a feasible formation pathway. CNTs and cationic CNTs, as well as their hydrogenated counterparts, exhibit intense vibrational transitions in the IR. Their possible presence in the ISM could be investigated by comparing the calculated vibrational spectra with astronomical observations made by the Infrared Space Observatory, Spitzer Space Telescope, and particularly the upcoming James Webb Space Telescope.

• 21.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Formation of polyynes and ring-polyyne molecules following fragmentation of polycyclic aromatic hydrocarbons2019In: Monthly notices of the Royal Astronomical Society, ISSN 0035-8711, E-ISSN 1365-2966, Vol. 486, no 2, p. 1875-1881Article in journal (Refereed)

In this work, we perform molecular dynamic (MD) simulations to investigate the stability and fragmentation processes of vibrationally excited linear polycyclic aromatic hydrocarbons (PAHs). The program of CP2K in combination with the semi-empirical method PM3 is utilized for the MD simulations. The simulations show that the formation of molecular hydrogens (H-2) is different than previous studies, in particular, different than compact PAHs. At high temperatures, linear PAHs tend to open aromatic rings and convert the sp(3) C-C or sp(2) C=C bonds to sp C C bonds by removing H-2; i.e. polyynes are formed in such process. Besides polyynes, PAHs attached with sp-bonded polyyne chains are commonly observed at high temperatures. We notice that due to the addition of flexible tails (polyynes), the ring-polyyne molecules do not dissociate for a long period of time at high temperatures. Such structures facilitate the molecules to survive in the harsh environment of the interstellar medium. In addition, the ring-polyyne structures induce dipole moments that could, in principle, be detected by radio astronomy.

• 22.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Missouri, Dept Phys & Astron, Columbia, MO 65211 USA..
Fragmentation and isomerization of polycyclic aromatic hydrocarbons in the interstellar medium: Coronene as a case study2020In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 633, article id A103Article in journal (Refereed)

Aims. Due to the limitations of current computational technology, the fragmentation and isomerization products of vibrationally-excited polycyclic aromatic hydrocarbon (PAH) molecules and their derivatives have been poorly studied. In this work, we investigate the intermediate products of PAHs and their derivatives as well as the gas-phase reactions relevant to the interstellar medium, with coronene as a case study. Methods. Based on the semi-empirical method of PM3 as implemented in the CP2K program, molecular dynamics simulations were performed to model the major processes (e.g., vibrations, fragmentations, and isomerizations) of coronene and its derivatives (e.g., methylated coronene, hydrogenated coronene, dehydrogenated coronene, nitrogen-substituted coronene, and oxygen-substituted coronene) at temperatures of 3000 K and 4000 K. Results. We find that the anharmonic effects are crucial for the simulation of vibrational excitation. For the molecules studied here, H-2, CO, HCN, and CH2 are the major fragments. Following the dissociation of these small units, most of the molecules could maintain their ring structures, but a few molecules would completely break into carbon chains. The transformation from a hexagon to a pentagon or a heptagon may occur and the heteroatomic substitutions (e.g., N- or O-substitutions) would facilitate the transformation.

• 23.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Sci & Technol China, Sch Chem & Mat Sci, Dept Chem Phys, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Anhui, Peoples R China. Univ Missouri, Dept Phys & Astron, Columbia, MO 65211 USA..
The infrared bands of polycyclic aromatic hydrocarbons in the 1.6-1.7 mu m wavelength region2019In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 632, article id A71Article in journal (Refereed)

Context. The 3.3 mu m aromatic C-H stretching band of polycyclic aromatic hydrocarbon (PAH) molecules seen in a wide variety of astrophysical regions is often accompanied by a series of weak satellite bands at similar to 3.4-3.6 mu m. One of these sources, IRAS 21282 +5050, a planetary nebula, also exhibits a weak band at similar to 1.68 mu m. While the satellite features at similar to 3.4-3.6 mu m are often attributed to the anharmonicities of PAHs, it is not clear whether overtones or combination bands dominate the 1.68 mu m feature. Aims. In this work, we examine the anharmonic spectra of eight PAH molecules, including anthracene, tetracene, pentacene, phenanthrene, chrysene, benz[a]anthracene, pyrene, and perylene, to explore the origin of the infrared bands in the 1.6-1.7 mu m wavelength region. Methods. Density functional theory (DFT) in combination with the vibrational second-order perturbation theory (VPT2) was used to compute the anharmonic spectra of PAHs. To simulate the vibrational excitation process of PAHs, the Wang-Landau random walk technique was employed. Results. All the dominant bands in the 1.6-1.7 mu m wavelength range and in the 3.1-3.5 mu m C-H stretching region are calculated and tabulated. It is demonstrated that combination bands dominate the 1.6-1.7 mu m region, while overtones are rare and weak in this region. We also calculate the intensity ratios of the 3.1-3.5 mu m C-H stretching features to the bands in the 1.6-1.7 mu m region, I3.1-3:5/I1.6-1.7, for both ground and vibrationally excited states. On average, we obtain < I3.1-3.5=/I1.6-1.7 > approximate to 12.6 and < I3.1-3.5=/I1.6-1.7 > approximate to 17:6 for PAHs at ground states and at vibrationally excited states, respectively.

• 24.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands..
Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands.. Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands.. NASA, Ames Res Ctr, Moffett Field, CA 94035 USA.. Leiden Univ, Leiden Observ, Niels Bohrweg 2, NL-2333 CA Leiden, Netherlands..
Anharmonicity and the infrared emission spectrum of highly excited polycyclic aromatic hydrocarbons2018In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 618, article id A49Article in journal (Refereed)

Aims. Infrared (IR) spectroscopy is a powerful tool to study molecules in space. A key issue in such analyses is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the IR spectra for molecules under various conditions. Methods. We combined second order vibrational perturbation theory and the Wang-Landau random walk technique to produce accurate IR spectra of highly excited polycyclic aromatic hydrocarbons. We fully incorporated anharmonic effects, such as resonances, overtones, combination bands, and temperature effects. Results. The results are validated against experimental results for the pyrene molecule (C16H10). In terms of positions, widths, and relative intensities of the vibrational bands, our calculated spectra are in excellent agreement with gas-phase experimental data.

• 25.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Photodissociation processes of Bisanthenquinone cation2017In: Proceedings of the International Astronomical Union, ISSN 1743-9213, no S332, p. 353-359Article in journal (Refereed)

A systematic study, using ion trap time-of-flight mass spectrometry, is presented for the photo-dissociation processes of Bisanthenquinone (Bq) cations, C28H12O2+, a ketone substituted Polycyclic Aromatic Hydrocarbon (PAH). The Bq cation fragments through sequential loss of the two neutral carbonyl (CO) units upon laser (626nm) irradiation, resulting in a PAH-like derivative C26H12+. Upon further irradiation, C26H12+ exhibits both stepwise dehydrogenation and C2/C2H2 loss fragmentation channels. Quantum chemistry calculations reveal a detailed picture for the first CO-loss, which involves a transition state with a barrier of ∼ 3.4 eV, which is lower than the energy required for the lowest H-loss pathway (∼ 5.0 eV). The barrier for the second CO-loss is higher (∼ 4.9 eV). The subsequent loss of this unit changes the Bq geometry from a planar to a bent one. It is concluded that the photodissociation mechanism of the substituted PAH cations studied here is site selective in the substituted subunit. This work also shows that an acetone substituted PAH cation is not photo-stable upon irradiation.

• 26. Chen, X.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
A unimolecular platform based on diarylethene with multiple stimuli-gated photochromism2019In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 164, p. 91-96Article in journal (Refereed)

The gated photochromic systems have attracted great interest in scientific researches due to their merits in the opto-electronic fields, whereas the multi-stimuli gating function in a unimolecular platform has rarely been addressed. Herein, a new strategy to realize multi-stimuli gated photochromic function was devised relying on a simple Schiff-based diarylethene derivative. The compound shows no photoswitching properties in solution under irradiation with any wavelength of light. It is noteworthy that mecury(II) ions, water and protons can trigger its photo-reactivity independently with different absorption changes, respectively. Therefore, a molecular logic circuit with four inputs, including mecury(II) ions, water, protons and UV light, was fabricated on the basis of the unimolecular platform, suggesting promise for application in multi-controlled photoswitchings. These results could be valuable for the further development of photoswitchings with multiple stimuli responses.

• 27.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
Kinetic Monte Carlo simulations of organic ferroelectrics2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 3, p. 1375-1383Article in journal (Refereed)

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.

• 28. Céolin, Denis
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effectManuscript (preprint) (Other academic)

Observing and controlling molecular motion, and in particular rotation,is a fundamental topic in physics and chemistry. In order toinitiate ultrafast rotation, one needs a way to transfer a large angularmomentum to the molecule. As a showcase, this was performedby hard x-ray C1s ionization of carbon monoxide, accompanied byspinning-up the molecule via the recoil “kick” of the emitted fast photoelectron.To visualize this molecular motion, we use the dynamicalrotational Doppler effect and an X-ray “pump-probe” device offeredby nature itself: the recoil-induced ultrafast rotation is probed by subsequentAuger electron emission. The time information in our experimentorigins from the natural delay between the C1s photoionizationinitiating the rotation and the ejection of the Auger electron. From amore general point of view, time-resolved measurements can be performedin two ways: either to vary the "delay" time as in conventionaltime-resolved pump-probe spectroscopy and to use the dynamicsgiven by the system, or to keep constant "delay" time and to manipulatethe dynamics. Since in our experiment we cannot change the delaytime given by the core-hole lifetime $\tau$, we use the second optionand control the rotational speed by changing the kinetic energy of thephotoelectron. The recoil-induced rotational dynamics controlled insuch a way is observed as a photon-energy dependent asymmetryof the Auger lineshape, in full agreement with theory. This asymmetryis explained by a significant change of the molecular orientationduring the core-hole lifetime, which is comparable with the rotationalperiod.

• 29.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Royal Inst Technol, Theoret Chem & Biol, S-10691 Stockholm, Sweden..
Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia.. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Royal Inst Technol, Theoret Chem & Biol, S-10691 Stockholm, Sweden.
Anomalous polarization dependence in vibrationally resolved resonant inelastic x-ray scattering of H2O2018In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 98, no 1, article id 012507Article in journal (Refereed)

It is well established that different electronic channels, in resonant inelastic x-ray scattering (RIXS), display different polarization dependences due to different orientations of their corresponding transition dipole moments in the molecular frame. However, this effect does not influence the vibrational progression in the Franck-Condon approximation. We have found that the transition dipole moments of core excitation and deexcitation experience ultrafast rotation during dissociation in the intermediate core-excited state. This rotation makes the vibrational progression in RIXS sensitive to the polarization of the x-ray photons. We study the water molecule, in which the effect is expressed in RIXS through the dissociative core-excited state where the vibrational scattering anisotropy is accompanied also by violation of parity selection rules for the vibrations.

• 30.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Lab Nonlinear Opt & Spect, Krasnoyarsk 660041, Russia. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.. Univ Zurich, Phys Chem Inst, CH-8057 Zurich, Switzerland.. Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden.. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Turku, Dept Phys & Astron, FI-20014 Turunyliopisto, Finland.. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland.. Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland.. Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland.. Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland.. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1013Article in journal (Refereed)

Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.

• 31.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.. Univ Turku, Dept Phys & Astron, FI-20014 Turun, Finland.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland.. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
Nuclear dynamics in resonant inelastic X-ray scattering and X-ray absorption of methanol2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 23, article id 234301Article in journal (Refereed)

We report on a combined theoretical and experimental study of core-excitation spectra of gas and liquid phase methanol as obtained with the use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The electronic transitions are studied with computational methods that include strict and extended second-order algebraic diagrammatic construction [ADC(2) and ADC(2)-x], restricted active space second-order perturbation theory, and time-dependent density functional theory-providing a complete assignment of the near oxygen K-edge XAS. We show that multimode nuclear dynamics is of crucial importance for explaining the available experimental XAS and RIXS spectra. The multimode nuclear motion was considered in a recently developed "mixed representation" where dissociative states and highly excited vibrational modes are accurately treated with a time-dependent wave packet technique, while the remaining active vibrational modes are described using Franck-Condon amplitudes. Particular attention is paid to the polarization dependence of RIXS and the effects of the isotopic substitution on the RIXS profile in the case of dissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to be due to an interplay between molecular and pseudo-atomic features arising in the course of transitions between dissociative core- and valence-excited states. The dynamical nature of the splitting of the 2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical results are in good agreement with our liquid phase measurements and gas phase experimental data available from the literature.

• 32.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). Peking Univ, Coll Chem & Mol Engn, Beijing 100871, Peoples R China.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. Peking Univ, Coll Chem & Mol Engn, Beijing 100871, Peoples R China.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
Water Oxidation Initiated by In Situ Dimerization of the Molecular Ru(pdc) Catalyst2018In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 8, no 5, p. 4375-4382Article in journal (Refereed)

The mononuclear ruthenium complex [Ru(pdc)L-3] (H(2)pdc = 2,6-pyridinedicarboxylic acid, L = N-heterocycles such as 4-picoline) has previously shown promising catalytic efficiency toward water oxidation, both in homogeneous solutions and anchored on electrode surfaces. However, the detailed water oxidation mechanism catalyzed by this type of complex has remained unclear. In order to deepen understanding of this type of catalyst, in the present study, [Ru(pdc)(py)(3)] (py = pyridine) has been synthesized, and the detailed catalytic mechanism has been studied by electrochemistry, UV-vis, NMR, MS, and X-ray crystallography. Interestingly, it was found that once having reached the Ru-IV state, this complex promptly formed a stable ruthenium dimer [Ru-III(pdc)(py)(2)-O-Ru-IV(pdc)(py)(2)](+). Further investigations suggested that the present dimer, after one pyridine ligand exchange with water to form [Ru-III(pdc)(py)(2)-O-Ru-IV(pdc)(py)(H2O)](+), was the true active species to catalyze water oxidation in homogeneous solutions.

• 33. Duan, S.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Effects of Plasmon Modes on Resonant Raman Images of a Single Molecule2020In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 11, no 2, p. 407-411Article in journal (Refereed)

Localized surface plasmons (LSPs) are excellent light sources at the nanoscale. How to precisely describe the interaction between LSPs and molecules has become an important issue. We present here a comprehensive study on the dependence of resonant Raman images on LSP modes generated by two typical nanostructures. Theoretical calculations demonstrate that the Raman images are sensitive to not only the spatial distribution but also the phase of the localized field, which should be attributed to the quantum nature of the interaction between LSP modes and molecules. We also find that the rotation of noncylindrical symmetry modes could affect the details of images, which offers an extra means to extract molecular information. Our findings extend the understanding of the LSP-matter interaction, which would be useful for the rational design of nanostructures and thus further applications of LSPs.

• 34.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Synerget Innovat Ctr Quantum Informat & Quantum P, Hefei 230026, Anhui, Peoples R China..
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre. Kaunas Univ Technol, Dept Phys, LT-51368 Kaunas, Lithuania.. Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Hebei, Peoples R China.. Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Synerget Innovat Ctr Quantum Informat & Quantum P, Hefei 230026, Anhui, Peoples R China..
Optomagnetic Effect Induced by Magnetized Nanocavity Plasmon2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 35, p. 13795-13798Article in journal (Refereed)

We propose a new type of optomagnetic effect induced by a highly confined plasmonic field in a nanocavity. It is shown that a very large dynamic magnetic field can be generated as the result of the inhomogeneity of nanocavity plasmons, which can directly activate spin-forbidden transitions in molecules. The dynamic optomagnetic effects on optical transitions between states of different spin multiplicities are illustrated by first-principles calculations for C-60. Remarkably, the intensity of spin forbidden singlet-to-triplet transitions can even be stronger than that of singlet-to-singlet transitions when the spatial distribution of plasmon is comparable with the molecular size. This approach not only offers a powerful optomagnetic means to rationally fabricate molecular excited states with different multiplicities but also provides a groundbreaking concept of the light-matter interaction that could lead to the observation of new physical phenomena and the development of new techniques.

• 35.
Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. PSI, Res Dept Synchrotron Radiat & Nanotechnol, CH-5232 Villigen, Switzerland.. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. PSI, Res Dept Synchrotron Radiat & Nanotechnol, CH-5232 Villigen, Switzerland.. Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden.. Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
One-dimensional cuts through multidimensional potential-energy surfaces by tunable x rays2018In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 97, no 5, article id 053410Article in journal (Refereed)

The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of our description of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.

• 36. Eckert, Sebastian
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
One-dimensional cuts through multidimensional potential energy surfaces by tunable X-rays2018Manuscript (preprint) (Other academic)

The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of ourdescription of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.

• 37. Elie, Margaux
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Role of the Bridging Group in Bis-Pyridyl Ligands: Enhancing Both the Photo- and Electroluminescent Features of Cationic (IPr) Cu-I Complexes2017In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 23, no 64, p. 16328-16337Article in journal (Refereed)

We report on the benefits of changing the bridging group X of bis-pyridyl ligands, that is, Py-X-Py where X is NH, CH2, C(CH3)(2), or PPh, on the photo-and electroluminescent properties of a new family of luminescent cationic H-heterocyclic carbene (NHC) copper(I) complexes. A joint experimental and theoretical study demonstrates that the bridging group affects the molecular conformation from a planar-like structure (X is NH and CH2) to a boat-like structure (X is C(CH3)(2) and PPh), leading to i) four-fold enhancement of the photoluminescence quantum yield (phi(em)) without affecting the thermally activated delayed fluorescence mechanism, and ii) one order of magnitude reduction of the ionic conductivity (sigma) of thin films. This leads to an overall enhancement of the device efficacy and luminance owing to the increased phi(em) and the use of low applied driving currents.

• 38.
Stockholm university.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Institut für Physik und Astronomie, Universität Potsdam. Research Department Synchrotron Radiation and Nanotechnology, Paul Scherrer Institut. Institute for Methods and Instrumentation in Synchrotron Radiation Research G- ISRR, Helmholtz-Zentrum Berlin für Materialien und Energie. Research Department Synchrotron Radiation and Nanotechnology, Paul Scherrer Institut. Institute for Methods and Instrumentation in Synchrotron Radiation Research G- ISRR, Helmholtz-Zentrum Berlin für Materialien und Energie. Institut für Physik und Astronomie, Universität Potsdam. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Stockholm university. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Ultrafast dissociation features in RIXS spectra of the water molecule2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)

In this combined theoretical and experimental study we report on an analysis of the resonant inelastic X-ray scattering spectra (RIXS) of gas phase water via the lowest dissociative core-excited state |1sO-14a11〉. We focus on the spectral feature near the dissociation limit of the electronic ground state. We show that the narrow atomic-like peak consists of the overlapping contribution from the RIXS channels back to the ground state and to the first valence excited state |1b1-14a11〉 of the molecule. The spectral feature has signatures of ultrafast dissociation (UFD) in the core-excited state, as we show by means of ab initio calculations and time-dependent nuclear wave packet simulations. We show that the electronically elastic RIXS channel gives substantial contribution to the atomic-like resonance due to the strong bond length dependence of the magnitude and orientation of the transition dipole moment. By studying the RIXS for an excitation energy scan over the core-excited state resonance, we can understand and single out the molecular and atomic-like contributions in the decay to the lowest valence-excited state. Our study is complemented by a theoretical discussion of RIXS in the case of the isotope substituted water (HDO and D2O) where the nuclear dynamics is significantly affected by the heavier fragments' mass.

• 39.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Derivation and application of response functions for nonlinear absorption and dichroisms2018Doctoral thesis, comprehensive summary (Other academic)

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.

• 40.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
A QM/MM and QM/QM/MM study of Kerr, Cotton-Mouton and Jones linear birefringences in liquid acetonitrile2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 5, p. 3831-3840Article in journal (Refereed)

QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear birefringences Kerr, Cotton-Mouton, and Jones, as shown by acetonitrile in the gas and pure liquid phases. The relevant first-order properties as well as linear, quadratic, and cubic frequency-dependent response functions were computed using time-dependent Kohn-Sham density-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 which averaged values of the observables were obtained at an optical wavelength of 632.8 nm. The birefringences were computed for electric and magnetic induction fields corresponding to the laboratory setup previously employed by T. Roth and G. L. J. A. Rikken in Phys. Rev. Lett., 2000, 85, 4478. Under these conditions, acetonitrile is shown to exhibit a weak Jones response-in fact roughly 6.5 times smaller than the limit of detection of the apparatus employed in the measurements mentioned above. A comparison is made with the corresponding gas-phase results and an assessment is made of the index of measurability, estimating the degree of overlap of the three birefringences in actual measurements. For acetonitrile, it is shown that this index is a factor of 3.6 and 6.7 larger than that of methylcyclopentadienyl-Mn-tricarbonyl and cyclohexadienyl-Fe-tricarbonyl, respectively-two compounds reported in Phys. Rev. Lett., 2000, 85, 4478 to exhibit a strong Jones signal.

• 41.
RAS, Kirensky Inst Phys Fed Res Ctr KSC SB, Krasnoyarsk 660036, Russia.;Fed Siberian Res Clin Ctr FMBA Russia, Krasnoyarsk 660037, Russia.;Siberian Fed Univ, Krasnoyarsk 660041, Russia..
Fed Siberian Res Clin Ctr FMBA Russia, Krasnoyarsk 660037, Russia.;Siberian Fed Univ, Krasnoyarsk 660041, Russia.;Reshetnev Siberian State Univ Sci & Technol, Krasnoyarsk 660037, Russia.. RAS, Kirensky Inst Phys Fed Res Ctr KSC SB, Krasnoyarsk 660036, Russia.;Siberian Fed Univ, Krasnoyarsk 660041, Russia.. RAS, Kirensky Inst Phys Fed Res Ctr KSC SB, Krasnoyarsk 660036, Russia.;Siberian Fed Univ, Krasnoyarsk 660041, Russia.. RAS, Kirensky Inst Phys Fed Res Ctr KSC SB, Krasnoyarsk 660036, Russia.;Siberian Fed Univ, Krasnoyarsk 660041, Russia.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Charge-transfer plasmons with narrow conductive molecular bridges: A quantum-classical theory2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 24, article id 244125Article in journal (Refereed)

We analyze a new type of plasmon system arising from small metal nanoparticles linked by narrow conductive molecular bridges. In contrast to the well-known charge-transfer plasmons, the bridge in these systems consists only of a narrow conductive molecule or polymer in which the electrons move in a ballistic mode, showing quantum effects. The plasmonic system is studied by an original hybrid quantum-classical model accounting for the quantum effects, with the main parameters obtained from first-principles density functional theory simulations. We have derived a general analytical expression for the modified frequency of the plasmons and have shown that its frequency lies in the near-infrared (IR) region and strongly depends on the conductivity of the molecule, on the nanoparticle-molecule interface, and on the size of the system. As illustrated, we explored the plasmons in a system consisting of two small gold nanoparticles linked by a conjugated polyacetylene molecule terminated by sulfur atoms. It is argued that applications of this novel type of plasmon may have wide ramifications in the areas of chemical sensing and IR deep tissue imaging. Published under license by AIP Publishing.

• 42.
Zhejiang Univ, Ctr Chem High Performance & Novel Mat, Dept Chem, Hangzhou 310027, Zhejiang, Peoples R China. u, Yao.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Zhejiang Univ, Dept Chem, Hangzhou 310027, Zhejiang, Peoples R China. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Duet of Acetate and Water at the Defects of Metal-Organic Frameworks2019In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 19, no 3, p. 1618-1624Article in journal (Refereed)

Metal-organic frameworks (MOFs) are porous crystalline materials with promising applications in molecular adsorption, separation, and catalysis. It has been discovered recently that structural defects introduced unintentionally or by design could have a significant impact on their properties. However, the exact chemical composition and structural evolution under different conditions at the defects are still under debate. In this study, we performed multidimensional solid-state nuclear magnetic resonance (SSNMR) coupled with computer simulations to elucidate an important scenario of MOF defects, uncovering the dynamic interplay between residual acetate and water. Acetate, as a defect modulator, and water, as a byproduct, are prevalent defect-associated species, which are among the key factors determining the reactivity and stability of defects. We discovered that acetate molecules coordinate to a single metal site monodentately and pair with water at the neighboring position. The acetates are highly flexible, which undergo fast libration as well as a slow kinetic exchange with water through dynamic hydrogen bonds. The dynamic processes under variable temperatures and different hydration levels have been quantitatively analyzed across a broad time scale from microseconds to seconds. The integration of SSNMR and computer simulations allows a precision probe into defective MOF structures with intrinsic dynamics and disorder.

• 43. Giussani, Angelo
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Molecular Basis of the Chemiluminescence Mechanism of Luminol2019In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, no 20, p. 5202-5213Article in journal (Refereed)

Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.

• 44.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004P. R. China.
Mechanistic Insight into the Binding Profile of DCVJ and alpha-Synuclein Fibril Revealed by Multiscale Simulations2019In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 10, no 1, p. 610-617Article in journal (Refereed)

Parkinson's disease (PD) is a serious neuro-degenerative disease and is characterized by abnormal alpha-synuclein (alpha-syn) accumulation in Lewy bodies (LB) and 2 Lewy neurites (LN), which makes alpha-syn an important imaging target for PD. An imaging probe that quantifies fibrillar alpha-syn can enhance the clinical diagnosis of PD and can also be used to evaluate the efficacy of therapeutics aimed at reducing the abnormal aggregation of the alpha-syn fibril in the brain. In this paper, we study the binding profile of fibrillar alpha-syn with a fluorescent probe 4-(dicyanovinyl)julolidine (DCVJ), which is being explored for identifying alpha-syn imaging agents. A multiscale simulation workflow including molecular docking, molecular dynamics, metadynamics, and QM/MM calculations was implemented. We find that DCVJ can bind to multiple sites of alpha-syn which are located either at the surface or in the core. Free energy calculations using implicit solvent models reveal that the most favorable binding mode for DCVJ is associated with the core binding site and is further confirmed by metadyamics simulation. Besides, a dynamic binding pathway is discovered, which reveals that DCVJ binds gradually into the core of the fibril passing through several intermediate states. The conformational arrest of the dicyano vinyl group in the fibrillar environment could explain the reason behind the fibril-specific fluorescence of DCVJ. Furthermore, based on hybrid QM/MM calculations, the molecular geometry of the dicyano vinyl group is found to be environment specific which explains why DCVJ serves as a staining agent for such fibrillar-like environments. Our results could be helpful for elucidating the binding mechanism of imaging tracers with the fibrillar form of alpha-syn and explain their fibrillar-specific optical properties, a knowledge that in turn can be used to guide the design and development of compounds with higher affinity and selectivity for alpha-syn using structure-based strategies.

• 45. Gusev, A. N.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
Synthesis and photophysical properties of Zn(II) Schiff base complexes possessing strong solvent-dependent solid-state fluorescence2018In: Polyhedron, ISSN 0277-5387, E-ISSN 1873-3719, Vol. 155, p. 202-208Article in journal (Refereed)

The present article reports on the syntheses, crystal structures and luminescence properties of three solvate forms of a zinc(II) complex containing 4-{(E)-[(2-fluorophenyl)imino]methyl}-5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one (HL). The reaction of zinc(II)acetate with the HL ligand in ethanol and acetonitrile led to the formation of two solvate analogues [Zn(L)2]·Solv (Solv – ethanol (1) and acetonitrile (2)). The properties of the [Zn(L)2]·Solv complexes were investigated by UV–Vis absorption and fluorescence emission spectroscopy, and the density functional theory calculations. Bader's topological analysis was performed to investigate the electronic peculiarities of Zn(II) polyhedra and non-covalent interactions within crystal packing of studied solvates.

• 46.
Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia. ryukova, Mariya.
Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Structure and excitation-dependent emission of novel zinc complexes with pyridyltriazoles2019In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 9, no 38, p. 22143-22152Article in journal (Refereed)

A series of Zn(ii) complexes with 5-(4-R-phenyl)-3-(pyridin-2-yl)-1,2,4-triazoles have been synthesized and subsequently characterized by single crystal X-ray diffraction, H-1-NMR, FT-IR spectroscopy, elemental analyses, ESI-MS, and PXRD. The X-ray diffraction analyses revealed that the complexes have a similar molecular structure and their supramolecular frameworks are constructed by hydrogen bonds and pi center dot center dot center dot pi interaction scaffolds. Upon irradiation with UV light, the studied complexes display deep blue emission at 396-436 nm in the solid state. The compounds show an unexpected excitation-dependent emission phenomenon which is detected by a change in the emission color (from blue to yellow) upon increase of the excitation wavelength. The conducted quantum-chemical calculations indicate that supramolecular differences in the single-crystal architecture of the synthesized complexes play a crucial role for this photophysical behaviour.

• 47.
Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia..
Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia.. Russian Acad Sci, NS Kurnakov Inst Gen & Inorgan Chem, Moscow 119991, Russia.. Lodz Univ Technol, Dept Mol Phys, Zeromskiego 116, PL-90924 Lodz, Poland.. Lodz Univ Technol, Dept Mol Phys, Zeromskiego 116, PL-90924 Lodz, Poland.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia.. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.. Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine.. Lviv Polytech Natl Univ, Stepan Bandera 12, UA-79013 Lvov, Ukraine.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia.. Vienna Univ Technol, Inst Appl Synthet Chem, Getreidemarkt 9-163 AC, A-1060 Vienna, Austria..
Novel Zinc Complex with an Ethylenediamine Schiff Base for High-Luminance Blue Fluorescent OLED Applications2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 18, p. 11850-11859Article in journal (Refereed)

To explore the photophysical properties of coordination compounds with bright blue fluorescence, an azomethin-zinc complex was synthesized and characterized by various techniques (elemental analysis, thermogravimetry, and IR-mass-spectroscopy). The crystal structure was determined by X-ray diffraction analysis. Through thermal characterization, this complex was proved to have good thermal stability. Photoluminescence spectra were recorded, both in solution and in the solid state, and the complexes showed noteworthy photoluminescence with a maximum in the blue region. The results of time-dependent density functional theory calculations indicated that the origin of luminescence for the title complex is a combination of monomer and excimer emissions. The light emission performance of the zinc complex in organic light emitting diodes was investigated, and the results indicated superior electroluminescence properties as a blue fluorescent light source (max. brightness 17 000 cd/m(2), max. EQE = 5%).

• 48.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry. KTH, Royal Institute of Technology.
Modeling environment effects on spectroscopic properties of biomarkers and catalytic mechanisms in enzymes2020Doctoral thesis, comprehensive summary (Other academic)

Arguably, humans are in need of both better diagnostic tools to prevent pro- gression of diseases as well as greener catalysts for synthesis of chemicals.

Neurodegenerative diseases affecting neurons in the brain leads to demen- tias, where Alzheimer’s disease (AD) is the most prevalent. It is estimated that about 50 million people worldwide suffer from AD, a number that has more than doubled during the last 30 years. Currently, there is no cure for AD, but in order to slow the progression of symptoms it is crucial to develop biomarkers for early detection and initiation of clinical interventions.

With theoretical tools it is possible to better understand the optical prop- erties of fluorescent biomarkers, and thus contribute to steering the design of biomarkers for distinguishing different types of disease-associated proteins. Lu- minescent conjugated oligothiophenes (LCO) is a class of molecules that binds to aggregates of misfolded amyloid-β proteins, facilitating in vivo-detection of the pathological hallmarks of AD. By performing molecular dynamics (MD) simulations and subsequent response theory calculations of a LCO, it could be concluded that the differences in the spectroscopic fingerprints for the bound and free biomarker were predominantly due to conformational changes of the conjugated π-system in the molecular backbone. The introduction of differ- ent central units with donor properties yield donor-acceptor-donor electronic systems that increase the range of spectroscopic detection of LCO biomark- ers, without reducing the selectivity towards amyloid-β. It was also revealed that in order to capture more of the two-photon absorption (TPA) signal it would be optimal to design biomarkers with the dominant TPA signal at longer wavelenghts.

The second part of this work is centered around computational enzyme design, and how single point mutations can alter the flow of water in the active site. The altered flow of water likely impacts the catalysis in the active site of the enzymes. The enzymes considered in this work belongs to two different enzyme classes, and catalyse different kinds of reactions. Squalene hopene cyclase (SHC) is a monotopic membrane enzyme that catalyses the cyclization of squalene to hopene, and ω-transaminase catalyses the transfer of an amino and keto group between an amino acid and a keto acid. Enzyme variants of both SHC and ω-transaminase, where single-point mutations have been introduced, display different experimentally observed properties compared to their corresponding wild-types (WT). By performing MD simulations, the flow of water in the active sites of both enzymes could be tracked. Distinct differences in the flow of water in the WT and enzyme variants could be detected. These changes are proposed to influence the catalysis, and help to explain the experimentally observed differences in the protein variants.

• 49.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
QM/MM Density Functional Theory Simulations of the Optical Properties Fingerprinting the Ligand-binding of Pentameric Formyl Thiophene Acetic Acid in Amyloid-β(1–42)Manuscript (preprint) (Other academic)
• 50.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Quantum Mechanics/Molecular Mechanics Density Functional Theory Simulations of the Optical Properties Fingerprinting the Ligand-Binding of Pentameric Formyl Thiophene Acetic Acid in Annyloid-beta(1-42)2020In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 124, no 5, p. 875-888Article in journal (Refereed)

The binding pocket proposed by Konig et al. [Chem. Commun. 2018, 54, 3030-3033] for the biomarker pentameric formyl thiophene acetic acid (p-FTAA) in the fibrillar structure of amyloid-beta(1-42) has been put to the test by the comparison of theoretical and experimental optical absorption and fluorescence spectra obtained in a water environment and inside the protein scaffold. The optical absorption/emission properties of this luminescent conjugated oligothiophene were studied by means of classical force field molecular dynamics simulations to account for the sampling of configuration space in conjunction with polarizable embedding time-dependent density functional theory calculations of spectra. The nuclear motions of residues in the beta-sheet were found to be modest, and the time dependence of embedding parameters was shown to be negligible so that a time-independent parameter set could be derived and used for all 300 snapshots considered in the spectrum averaging. In regard to linear absorption spectra, the calculated red shift due to protein binding for the dominant S-1 <- S-0 transition in p-FTAA was found to be equal to 23 nm (0.17 eV), which is in excellent agreement with the corresponding experimental result of 18 nm and taken as corroborating evidence for having correctly identified the binding pocket of p-FTAA in the amyloid. The underlying mechanisms for the calculated red shift were disentangled, and it is shown that some 20 nm (0.15 eV) of the total 23 nm (0.17 eV) is associated with increased planarity of p-FTAA in the binding pocket, whereas a mere 3 nm (0.02 eV) is associated with changes in the environment. In regard to emission spectra, we demonstrate that intersystem crossing from the excited S-1 state to the triplet manifold of states is a less likely event for p-FTAA in the binding pocket as compared to in the aqueous solution, and we thereby partly explain the much higher quantum yield of fluorescence for the more rigid p-FTAA in the binding pocket. Two-photon absorption in p-FTAA is shown to predominantly occur to an overall symmetric excited state and be more than twice as strong for the biomarker in the binding pocket as compared to in water. The corresponding red shift, on the other hand, is very small. Earlier experimental two-photon fluorescence imaging using p-FTAA is shown not to target the dominant two-photon state, and ways to reach a higher image quality (lower signal-to-noise ratio) are proposed in terms of tuning the laser wavelength toward the region of 600 nm or the synthesis of asymmetric ligands with S-1 states that are both one- and two-photon allowed.

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• rtf