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• 1151.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Quantum Nuclear Dynamics in Resonant X-ray Scattering of Gas-Phase and Liquid Systems2018Doctoral thesis, comprehensive summary (Other academic)

This thesis focuses on the role of the nuclear degrees of freedom in X-ray induced molecular processes. An important part of it is devoted to establishing theoretical principles to model and interpret high-resolution resonant X-ray scattering experiments in gases and liquids. Our investigations address the resonant inelastic x-ray scattering (RIXS) of H2O(g), H2O(l) and CH3OH(g) and Auger emission induced by hard X-rays in CO(g). The simulations for gas-phase systems are based on a multi-mode wave packet formalism and on potential energy surfaces computed with multi-configurational approaches.

For liquid systems, we propose a classical/quantum formalism for simulating RIXS based on a combination of ab initio molecular dynamics, density functional theory calculations and quantum nuclear wave packet propagation. The developed model is able to reproduce the experimental observation of shortening of the vibrational progression in H2O(l).

We show that electronically-elastic RIXS has an intrinsic capability to map the potential energy surface and to carry out vibrational analysis of the electronic ground state in free molecules as well as liquids. For gas-phase water, we see that the landscape of different core-excited states cause the nuclear wave packet to be localized along specific directions thus allowing to reconstruct one-dimensional potential energy curves. For liquid water, we propose a model for deriving, from experiment, confidence intervals for the molecular potential energy curves along the OH bonds, which are determined by the local arrangement of the hydrogen bond network.

We also investigate the role of ultra-fast rotations induced by photoionization by hard X-rays. In this case, the ejection of a fast photoelectron results in an ultra-fast rotational motion of the molecule, which combined with the anisotropy of the Auger process causes the spectral profile to be split due to a dynamical Doppler effect.

• 1152.
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. 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.
Anomalous polarization dependence in vibrationally resolved RIXS of H2OManuscript (preprint) (Other academic)

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 de-excitation experience ultrafast rotation during the dissociation in intermediate core-excited state. This rotations makes the vibrational progression in RIXS spectra sensitive to the polarisation of the X-ray photons. The studied effect is exemplified for the RIXS of the water molecule through the dissociative core-excited state where the vibrational scattering anisotropy is accompanied also by violation of parity selection rules for vibrations.

• 1153.
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. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scatteringManuscript (preprint) (Other academic)

The potential energy surface is widely used powerful concept in chemical physics. However, direct experimental access to the local potential energy surface in liquid especially in systems  with strong hydrogen bonds is lacking. We develop general technique demonstrated  for liquid water how to reconstruct from state-of-the-art  sub-natural linewidth resonant inelastic X-ray scattering (RIXS)  the local distribution of OH potential energy curves,  separately for OH bonds with weak and strong hydrogen bond. By this we are able to look on the local structure by characterising  selectively the strength of the hydrogen bond. We present a detailed analysis of the formation of the vibrationally resolved RIXS of liquids using a classical/quantum formalism  based on a combination of {\it ab initio} molecular dynamics, density functional theory calculations and quantum nuclear wave packet propagation. Theory nicely explains shortening of the vibrational progression in liquid phase in comparison with RIXS of free water molecules seen in the experiment by fluctuation of the hydrogen bond  network and coherent excitation of both OH bonds.

• 1154.
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. 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. 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.
Resonant inelastic X-ray scattering and X-ray absorption of methanol at the near oxygen K-edgeManuscript (preprint) (Other academic)

We report on a theoretical analysis of core-excitation spectra of gas and liquid phase methanol asobtained with use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering(RIXS). The electronic transitions are studied with complementary computational methods includ-ing strict and extended second-order algebraic diagrammatic construction (ADC(2) and ADC(2)-x),restricted active space second-order perturbation theory (RASPT2), and time-dependent densityfunctional theory (TDDFT)—providing a complete assignment of the near oxygen K-edge XAS.We show that multimode nuclear dynamics is of crucial importance for explaining the availableexperimental XAS and RIXS spectra. Multimode nuclear motions was considered in a developedmixed representation where dissociative states and highly excited vibrational modes are accuratelytreated with a time-dependent wave packet technique while the remaining active vibrational modesare described using Franck–Condon amplitudes. Particular attention is paid to the polarizationdependence of RIXS and the effects of the isotope substitution on the RIXS profile in the case ofdissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to bedue to an interplay between molecular and atomic-like features arising in the course of transitionsbetween dissociative core- and valence-excited states. The dynamical nature of the splitting of the2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical resultsare in good agreement with available experimental data.

• 1155.
KTH, School of Biotechnology (BIO).
Modeling of methyl transfer reactions in S-Adenosyl-L-Methionine dependent enzymes2006Licentiate thesis, comprehensive summary (Other scientific)

A very important trend for studying biomolecules is computational chemistry. In particular, nowadays it is possible to use theoretical methods to figure out the catalytic mechanism of enzyme reactions. Quantum chemistry has become a powerful tool to achieve a description of biological processes in enzymes active sites and to model reaction mechanisms.

The present thesis uses Density Functional Theory (DFT) to investigate catalytic mechanism of methyltransferase enzymes. Two enzymes were studied – Glycine N-MethylTransferase (GNMT) and Guanidinoacetate Methyltransferase (GAMT). Different models of the enzyme active sites, consisting of 20 to 100 atoms, are employed. The computed energetics are compared and are used to judge the feasibility of the reaction mechanisms under investigation.

For the GNMT enzyme, the methyl transfer reaction was found to follow an SN2 reaction mechanism. The calculations demonstrate that the mechanism is thermodynamically reasonable. Based on the calculations it was concluded that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to carboxylate group raise the barrier.

In the GAMT enzyme the methyl transfer reaction was found to follow a concerted asynchronous mechanism which includes transfer of a methyl group accompanied by a proton transfer taking place simultaneously in the same kinetic step. The calculated barrier agrees well with the experimental rate constant. i

• 1156.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Methyl transfer in glycine N-methyltransferase: a theoretical study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 16, p. 8216-8219Article in journal (Refereed)

Density functional theory calculations using the hybrid functional B3LYP have been performed to study the methyl transfer step in glycine N-methyltransferase (GNMT). This enzyme catalyzes the S-adenosyl-l-methionine (SAM)-dependent methylation of glycine to form sarcosine. The starting point for the calculations is the recent X-ray crystal structure of GNMT complexed with SAM and acetate. Several quantum chemical models with different sizes, employing up to 98 atoms, were used. The calculations demonstrate that the suggested mechanism, where the methyl group is transferred in a single SN2 step, is thermodynamically plausible. By adding or eliminating various groups at the active site, it was furthermore demonstrated that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to the carboxylate group raise the barrier.

• 1157.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Theoretical study of the methyl transfer in guanidinoacetate methyltransferase2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 1, p. 16-19Article in journal (Refereed)

The reaction mechanism of the guanidinoacetate methyltransferase (GAMT) enzyme has been investigated by means of density functional theory using the B3LYP hybrid functional. GAMT catalyzes the S-adenosyl-l-methionine (SAM)-dependent methylation of guanidinoacetate (GAA) to form creatine. A quantum chemical model was built on the basis of the recent crystal structure of GAMT complexed with S-adenosylhomocysteine (SAH) and GAA. The methyl group transfer from SAM to NE of GAA is shown to occur concertedly with a proton transfer from NE to the neighboring OD1 of Asp134. Good agreement is found between the calculated barrier and the experimental rate.

• 1158.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Quantum nuclear dynamics in  x-ray scattering and lasing2008Doctoral thesis, comprehensive summary (Other scientific)

This thesis presents a theoretical study of the role of nuclear degrees of freedom in the x-ray absorption, x-ray resonant scattering  and some aspects of the interaction of matter with strong laser fields. Most numerical simulations are performed with a time-dependent wave-packet program that have proved its robustness  in previous investigations. The relevant experimental results are also presented for comparison when available.

The first problem considered in the thesis is the possibility of obtaining x-ray absorption spectra with resolution beyond the natural lifetime broadening of the core-excited electronic states. It is shown that the method of measuring x-ray absorptionin the resonant scattering mode suggested earlier for that purpose exhibits severe limitations originating from the lifetime vibrational interference between the intermediate core-excited vibrational levels. However, a broad class of molecules is found for which spectra with super-high resolution can indeed be obtained. These molecules have parallel potential energy surfaces of the core-excited and final states for the x-ray scattering process.

The interpretations of two interesting cases of x-ray absorption and Auger scattering follow. The first one is related to scattering through a doubly excited Π state in the CO molecule. A Doppler split feature near 299.4 eV and strong scattering anisotropy are  observed. Both features are well explained and reproduced by the theory. Next, theelectron-vibrational fine structure of the $O1s\rightarrow\sigma^{*}$ excitation for O2 is investigated by means of different models. We are able to single out the electronic states and interpotential crossing points responsible for the peculiar absorption profile. Based on these findings we explain and reproduce the x-ray Auger scattering spectra through the same excitation. Here we encounter a rather unusual situation in which the Auger spectra are affected by three types of the interference: Apart from the lifetime vibrational interference, a strong interference between two intermediate electronic states and an interference with the direct-scattering amplitude is also present.

The process of intramolecular vibrational redistribution (IVR) is investigated in the context of formation of amplified spontaneous emissions (ASE) inside laser-pumped gain media. IVR raises to a higher energy region the threshold pump intensity after which blue-shifted ASE is observed.

Finally, we suggest a new scheme of x-ray pump-probe spectroscopy based on the core-hole hopping in N2 induced by an infrared laser field. We investigate the result from the core-hole hoping on the vibrational structure of the x-ray absorption profile. Furthermore, by populating core-excited states with opposite parities, the laser field opens up symmetry forbidden resonant inelastic scattering channels, which can give new insights about the electronic structure of matter.

• 1159.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
UVSOR Facility, Institute for Molecular Science, Okazaki. UVSOR Facility, Institute for Molecular Science, Okazaki. KTH, School of Biotechnology (BIO), Theoretical Chemistry. KTH, School of Biotechnology (BIO), Theoretical Chemistry.
X-ray absorption spectroscopy measured in resonant X-ray scattering mode: How unnatural is the resolution beyond the natural width?2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 465, no 1-3, p. 153-156Article in journal (Refereed)

The aim of this work is to give a clarifying view of the ‘super-high resolution’ scheme employing X-ray absorption spectroscopy in the resonant scattering mode. If the idea is not applied carefully, unrealistic results, as ‘perfect’ resolution, can be produced. The background of the problem is that the technique of extracting lifetime-broadening-free spectra assumes a known location of the resonance in the two-dimensional map of X-ray scattering spectra. The accuracy of the latter is, however, related to the lifetime broadening of the core-excited state. Thus, a compromise must be found between the uncertainty in the position of the X-ray absorption peak and the width of the desired absorption profile.

• 1160.
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
Limitations of X-ray absorption spectroscopy of super-high resolution measured in resonant Auger modeArticle in journal (Other academic)
• 1161.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
KTH, School of Biotechnology (BIO), Theoretical Chemistry. KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Pseudo-resonance formation in X-ray absorption spectrum of oxygen moleculeManuscript (Other academic)
• 1162.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
KTH, School of Biotechnology (BIO), Theoretical Chemistry. KTH, School of Biotechnology (BIO), Theoretical Chemistry. KTH, School of Biotechnology (BIO), Theoretical Chemistry. KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Role of intramolecular vibrational redistribution on dynamics of cavityless lasingManuscript (Other academic)
• 1163.
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
X-ray absorption of N2 accompanied by infrared-induced transitions between the ungerade and gerade core levels2008In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 41, no 14, p. 145601-Article in journal (Refereed)

We study a two-colour pump–probe scheme of x-ray absorption accompanied by core-hole hopping in the field of a strong IR laser. The process is exemplified for fixed-in-space and randomly oriented homonuclear diatomic molecules N2 near the 1σu → 1πg x-ray absorption transition. The laser field mixes the core holes of opposite parities and causes Rabi splitting of the core-excited states. The IR field results in spectral broadening and shifts of the x-ray resonances as well as decrease of x-ray photoabsorption. The Stark broadening of the x-ray absorption spectrum depends on the orientation of the molecule and the angle between the polarization vectors of the x-ray and IR fields. The spectral changes caused by the IR field are weaker for randomly oriented molecules in comparison with fixed-in-space molecules.

• 1164. Vigo-Aguiar, J.
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
Mathematical and computational tools in theoretical chemistry2009In: Journal of Mathematical Chemistry, ISSN 0259-9791, E-ISSN 1572-8897, Vol. 48, no 1, p. 1-2Article in journal (Other academic)
• 1165. Villaume, S.
Linköping University, Sweden.
Near sulfur L-edge X-ray absorption spectra of methanethiol in isolation and adsorbed on a Au(111) surface: A theoretical study using the four-component static exchange approximation2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 21, p. 5596-5601Article in journal (Refereed)

The relativistic four-component static exchange approach for calculation of near-edge X-ray absorption spectra has been reviewed. Application of the method is made to the Au(111) interface and the adsorption of methanethiol by a study of the near sulfur L-edge spectrum. The binding energies of the sulfur 2p 1/2 and 2p3/2 sublevels in methanethiol are determined to be split by 1.2 eV due to spin-orbit coupling, and the binding energy of the 2p3/2 shell is lowered from 169.2 eV for the isolated system to 167.4 and 166.7-166.8 eV for methanethiol in mono- and di-coordinated adsorption sites, respectively (with reference to vacuum). In the near L-edge X-ray absorption fine structure spectrum only the σ*(S-C) peak at 166 eV remains intact by surface adsorption, whereas transitions of predominantly Rydberg character are largely quenched in the surface spectra. The σ*(S-H) peak of methanethiol is replaced by low-lying, isolated, σ*(S-Au) peak(s), where the number of peaks in the latter category and their splittings are characteristic of the local bonding situation of the sulfur.

• 1166. Villaume, S.
Linköping University, Sweden.
On circular dichroism and the separation between chromophore and chiral center: The near carbon K-Edge X-ray absorption and circular dichroism spectra of noradrenaline and L-DOPA2009In: Chirality, ISSN 0899-0042, E-ISSN 1520-636X, Vol. 21, no 1 E, p. E13-E19Article in journal (Refereed)

The near carbon K-edge X-ray absorption and circular dichroism spectra of noradrenaline (neutral and protonated forms) and L-DOPA (protonated form) have been determined with use of the complex polarization propagator method in conjunction with Kohn-Sham density functional theory. A Coulomb attenuated exchange-correlation functional and London atomic orbitals have been employed to address the issues of hole-electron interactions and gauge-origin dependence of the magnetic-dipole operator, respectively. Results show that the characteristics of the chromophore part of the circular dichroism spectra are shared for all three considered systems, whereas protonation qualitatively alters the part of the spectrum assigned to the chiral side chain. The comparatively larger spatial separation of chromophore and chiral center in L-DOPA inflicts larger differences in spectral intensities between the chromophore and chiral center part of the circular dichroism spectra.

• 1167. Villaume, S.
Linköping University, Sweden.
Linear complex polarization propagator in a four-component Kohn-Sham framework2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 6, article id 064105Article in journal (Refereed)

An algorithm for the solution of the linear response equation in the random phase approximation is presented. All entities including frequency arguments, matrices, and vectors, are assumed to be complex, and it represents the core equation solver needed in complex polarization propagator approaches where nonstimulated relaxation channels are taken into account. Stability and robustness of the algorithm are demonstrated in applications regarding visible, ultraviolet, and x-ray spectroscopies. An implementation of the algorithm at the level of four-component relativistic, noncollinear, density functional theory for imaginary (but not complex) frequency arguments has been achieved and is used to determine the electric dipole dispersion interaction coefficients for the rubidium and cesium dimers. Our best estimates for the C6 coefficients of Rb2 and Cs2 are equal to 14.0× 103 and 21.9× 103 a.u., respectively.

• 1168.
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, Faculty of Science & Engineering.
Modelling Charge Transport for Organic Solar Cells within Marcus Theory2017Doctoral thesis, comprehensive summary (Other academic)

With the technological advancement of modern society, electronic devices are getting progressively more integrated in our everyday lives. Their continuouslygrowing presence is generating numerous concerns about costs, efficiency and the environmental impact of the electronic waste. In this context, organic electronics is finding its way through the market, allowing for potentially low-cost, light, flexible, transparent and environmentally friendly electronics. Despite the numerous successes of organic electronics, the functioning of several categories of organic devices still represents a technological challenge, due to problems like low efficiencies and stabilities (degradation over time).

Organic devices are composed by one or more organic materials depending on the particular application. The conformation and electronic structure of the organic molecules as well as their supramolecular arrangement in the single phase or at the interface are known to strongly a affect the mobility and/or the efficiency of the device. While there is consensus on the fundamental physics of organic devices, we still lack a detailed comprehensive theory able to fully explain experimental data. In this thesis we focus on trying to expand our knowledge of charge transport in organic materials through theoretical modelling and simulation of organic electronic devices. While the methodology developed is generally valid for any organic device, we will particularly focus on the case represented by organic photovoltaics.

The morphology of the system is obtained by molecular dynamics simulations. Marcus theory is used to calculate the hopping rate of the charge carriers and subsequently study the possibility of free charge carriers production in an organic solar cell. The theory is then compared both with Kinetic Monte Carlo simulations and with experiments to identify the main pitfalls of the actual theory and ways to improve it. The Marcus rate between two molecules depends on the molecular orbital energies, the transfer integral between the two molecules and the reorganization energy. The orbital energies and the transfer integrals between two neighbouring molecules are obtained through quantum mechanical calculations in vacuum. Electrostatic effects of the environment are included through atomic charges and atomic polarizabilities, producing a correction both to the orbital energy and to the reorganization energy. We have studied several systems in the single phase (polyphenylene vinylene, C60, PC61BM) and at the interface between two organic materials (anthracene/C60, TQ1/PC71BM).

We show how a combination of different methodologies can be used to obtain a realistic ab-initio model of organic devices taking into account environmental effects. This allows us to obtain qualitative agreement with experimental data of mobility in the single phase and to determine whether or not two materials are suitable to be used together in an organic solar cell.

• 1169.
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
University of Brasilia, Brazil. University of Brasilia, Brazil. University of Malaga, Spain. CSIC, Spain. University of Malaga, Spain. Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
Modelling charge transport of discotic liquid-crystalline triindoles: the role of peripheral substitution2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 35, p. 24202-24208Article in journal (Refereed)

We have performed a multiscale approach to study the influence of peripheral substitution in the semiconducting properties of discotic liquid-crystalline triindoles. Charge carrier mobility as high as 1.4 cm(2) V-1 s(-1) was experimentally reported for triindoles substituted with alkynyl chains on the periphery (Gomez-Lor et al. Angew. Chem., Int. Ed., 2011, 50, 7399-7402). In this work, our goal is to get a deeper understanding of both the molecular electronic structure and microscopic factors affecting the charge transport properties in triindoles as a function of the spacer group connecting the central cores with the external alkyl chains (i.e., alkyne or phenyl spacers groups). To this end, we first perform Quantum Mechanical (QM) calculations to assess how the peripheral substitution affects the electronic structure and the internal reorganization energy. Secondly, boxes of stacked molecules were built and relaxed through molecular dynamics to obtain realistic structures. Conformational analysis and calculations of transfer integrals for closed neighbours were performed. Our results show that the insertion of ethynyl spacers between the central aromatic core and the flexible peripheral chains results in lower reorganization energies and enhanced intermolecular order within the stacks with a preferred cofacial 60 degrees staggered conformation, which would result in high charge-carrier mobilities in good agreement with the experimental data. This work allows a deeper understanding of charge carrier mobility in columnar phases, linking the structural order at the molecular level to the property of interest, i.e. the charge carrier mobility. We hope that this understanding will improve the design of systems at the supramolecular level aiming at obtaining a more defined conducting channel, higher mobility and smaller fluctuations within the column.

• 1170.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Exploring Hydrogen Storage in PEDOT: A Computational Study2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 4, p. 2066-2074Article in journal (Refereed)

A reliable hydrogen-based energy technology requires promising materials for safe storage and transport of hydrogen. Here, the storage of hydrogen in the organic polymer poly(3,4-ethylenedioxythiophene) (PEDOT) is explored using density functional theory calculations. It is demonstrated that hydrogen chemisorption on PEDOT is feasible with the maximum gravimetric uptake of similar to 2.8 wt % in ambient condition, whereas physisorption is possible only at very low temperatures or at high pressure. The Gibbs absorption energies, electronic structure, and absorption spectra are calculated for the cases of chemisorption of a single hydrogen atom, a hydrogen pair, and hydrogen saturated chain for both neutral and oxidized PEDOT. Various experimental routes for PEDOT hydrogenations are discussed.

• 1171.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
Phase-Transferable Force Field for Alkali Halides2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed)
• 1172.
KTH, Superseded Departments, Biotechnology.
KTH, Superseded Departments, Biotechnology. Department of Physics, Shandong Normal University, Jinan. KTH, Superseded Departments, Biotechnology.
Solvent dependence of solvatochromic shifts and the first hyperpolarizability of para-nitroaniline: a nonmonotonic behaviour2003In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 119, no 8, p. 4409-Article in journal (Refereed)

Solvent dependence of the electronic structure and nonlinear optical properties of the para-nitroaniline (pNA) molecule on the polarity of the solutions has been studied using the polarizable continuum model in combination with the hybrid density functional theory. With a supermolecular approach, specific hydrogen bonding effects have also been fully considered. Good agreement between theory and experiments are obtained for both solvatochromic shifts of the charge transfer state and the solvent-induced first hyperpolarizability of pNA.

• 1173. Wang, G.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Shandong Normal University, China. KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
Theoretical identification of C34 isomers by XPS and NEXAFS spectra2016In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 644, p. 111-116Article in journal (Refereed)

Six C34 isomers were theoretically identified by X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra. The XPS and NEXAFS spectra of K-edge for all non-equivalent carbon atoms were simulated by density functional theory method combined with the full core-hole potentials. The XPS spectra mainly showed dependence on the isomers with different symmetries. Strong isomer identification of the NEXAFS spectra for C34 was found and discussed in detail. Furthermore, the spectra components of carbon atoms with different local environment were explored. The NEXAFS spectra dependence on the local structure of fullerene was discussed as well.

• 1174.
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
Light-driven rotary molecular motors without point chirality: a minimal design2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 10, p. 6952-6956Article in journal (Refereed)

A fundamental requirement for achieving photoinduced unidirectional rotary motion about an olefinic bond in a molecular motor is that the potential energy surface of the excited state is asymmetric with respect to clockwise and counterclockwise rotations. In most available light-driven rotary molecular motors, such asymmetry is guaranteed by the presence of a stereocenter. Here, we present non-adiabatic molecular dynamics simulations based on multi-configurational quantum chemistry to demonstrate that this chiral feature is not essential for inducing unidirectional rotary motion in molecules that incorporate a cyclohexenylidene moiety into a protonated Schiff-base framework. Rather, the simulations show that it is possible to exploit the intrinsic asymmetry of the puckered cyclohexenylidene to control the direction of photoinduced rotation.

• 1175.
Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China..
Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai Synchrotron Radiat Facil, Shanghai 201204, Peoples R China.. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China.. Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China.. Chinese Acad Sci, Shanghai Inst Appl Phys, Shanghai Synchrotron Radiat Facil, Shanghai 201204, Peoples R China.. Zhejiang Univ, Zhejiang Prov Key Lab Adv Chem Engn Mfg Technol, Coll Chem & Biol Engn, Hangzhou 310027, Zhejiang, Peoples R China..
Electrochemical and Spectroscopic Study of Homo- and Hetero-Dimetallic Phthalocyanines as Catalysts for the Oxygen Reduction Reaction in Acidic Media2018In: CHEMELECTROCHEM, ISSN 2196-0216, Vol. 5, no 22, p. 3478-3485Article in journal (Refereed)

Metallophthalocyanines (MPc, M=Fe or Co) have been investigated extensively as a typical type of transition metal macrocyclic catalysts for the oxygen reduction reaction (ORR). However, the understanding about ORR catalyzed by binuclear even heterodimetallic phthalocyanines in acidic condition is still not sufficient. Herein we synthesized two homodimetallicphthalocyanine (FePc-PcFe and CoPc-PcCo) and a heterodimetallic phthalocyanine (FePc-PcCo). The electrocatalytic activity of as-synthesized compounds were characterized by cyclic voltammetry (CV) and rotating disk electrode (RDE). Generally, the binuclear metallophthalocyanines show higher activity than their monomeric analogues including FePc and CoPc. Also, the Fe compounds exhibit better catalytic performance than the Co phthalocyanines. However, interestingly the heterodimetallic phthalocyanine FePc-PcCo shows similar half-wave potential and ORR activity with FePc-PcFe, rather than CoPc-PcCo. This may be explained by XPS and XAS, which reveal a similar square-planar structure existed in FePc-PcCo and FePc-PcFe and a non-planar structure in CoPc-PcCo. Furthermore, the increasing of the ORR activity among those five catalysts is well in agreement with the descending LUMO energies in DFT calculations. A lower LUMO energy indicates a favorable adsorption of O-2, which in turn affects the ORR performance.

• 1176. Wang, Xiaolin
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Comprehension of the Effect of a Hydroxyl Group in Ancillary Ligand on Phosphorescent Property for Heteroleptic Ir(III) Complexes: A Computational Study Using Quantitative Prediction2017In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 56, no 15, p. 8986-8995Article in journal (Refereed)

A new Ir(III) complex (dfpypya)(2)Ir(pic-OH) (2) is theoretically designed by introduction of a simple hydroxyl group into the ancillary ligand on the basis of (dfpypya)(2)Ir(pic) (1) with the aim to get the high efficiency and stable blue-emitting phosphors, where dfpypya is 3-methyl-6-(2',4'-difluoro-pyridinato)pyridazine, pic is picolinate, and pic OH is 3-hydroxypicolinic acid. The other configuration (dfpypya)(2)Ir(pic OH)' (3) is also investigated to compare with 2. The difference between 2 and 3 is whether the intramolecular hydrogen bond is formed in the (dfpypya)(2)Ir(pic OH). The quantum yield is determined by three different methods including the semiquantitative and quantitative methods. To quantitatively determine the quantum yield is still not an easy task to be completed. This work would provide some useful advices to select the suitable method to reliably evaluate the quantum yield. Complex 2 has larger quantum yield and more stability as compared with 1 and 3. The formation of intramolecular hydrogen bond would become a new method to design new phosphor with the desired properties.

• 1177.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Computational Studies of Structures and Binding Properties of Protein-Ligand Complexes2017Doctoral thesis, comprehensive summary (Other academic)

Proteins are dynamic structural entities that are involved in many biophysical processes through molecular interactions with their ligands. Protein-ligand interactions are of fundamental importance for computer-aided drug discovery. Due to the fast development in computer technologies and theoretical methods, computational studies are by now able to provide atomistic-level description of structures, thermodynamic and dynamic properties of protein-ligand systems, and are becoming indispensable in understanding complicated biomolecular systems. In this dissertation, I have applied molecular dynamic (MD) simulations combined with several state of the art free-energy calculation methodologies, to understand structures and binding properties of several protein-ligand systems.

The dissertation consists of six chapters. In the first chapter, I present a brief introduction to classical MD simulations, to recently developed methods for binding free energy calculations, and to enhanced sampling of configuration space of biological systems. The basic features, including the Hamiltonian equations, force fields, integrators, thermostats, and barostats, that contribute to a complete MD simulation are described in chapter 2. In chapter 3, two classes of commonly used algorithms for estimating binding free energies are presented. I highlight enhanced sampling approaches in chapter 4, with a special focus on replica exchange MD simulations and metadynamics, as both of them have been utilized in my work presented in the chapter thereafter. In chapter 5, I outlined the work in the 5 papers included in the thesis. In paper I and II, I applied, respectively, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and alchemical free energy calculation methods to identify the molecular determinant of the affibody protein ZAb3 bound to an amyloid b peptide, and to investigate the binding profile of the positive allosteric modulator NS-1738 with the α7 acetylcholine-binding protein (α7-AChBP protein); in paper III and VI, unbiased MD simulations were integrated with the well-tempered metadynamics approach, with the aim to reveal the mechanism behind the higher selectivity of an antagonist towards corticotropin-releasing factor receptor-1 (CRF1R) than towards CRF2R, and to understand how the allosteric modulation induced by a sodium ion is propagated to the intracellular side of the d-opioid receptor; in the last paper, I proved the structural heterogeneity of the intrinsically disordered AICD peptide, and then employed the bias-exchange metadynamics and kinetic Monte Carlo techniques to understand the coupled folding and binding of AICD to its receptor Fe65-PTB2. I finally proposed that the interactions between AICD and Fe65-PTB2 take place through an induced-fit mechanism. In chapter 6, I made a short conclusion of the work, with an outlook of computational simulations of biomolecular systems.

• 1178.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Exploring Biopolymer-Clay Nanocomposite Materials by Molecular Modelling2015Doctoral thesis, comprehensive summary (Other academic)

In this thesis, bio-nanocomposites made from two alternative biopolymers and montmorillonite (Mnt) clay have been investigated by molecular modelling. These biopolymers are xyloglucan (XG) and chitosan (CHS), both of which are abundant, renewable, and cost-effective. After being reinforced by Mnt clay nanoparticles, the polymer nanocomposites gains in multifunctionality and in the possibility to register unique combinations of properties, like mechanical, biodegradable, electrical, thermal and gas barrier properties. I apply molecular dynamics (MD) simulations to study the interfacial mechanisms of the adhesion of these biopolymers to the Mnt nanoplatelets at an atomic level.

For the XG-Mnt system, a strong binding affinity of XG to a fully hydrated Mnt interface was demonstrated. It was concluded that the dominant driving force for the interfacing is the enthalpy, i.e. the potential energy of the XG-Mnt interacting system. The adsorbed XG favors a flat conformation with a galactose residue in its side chain that facilitates the adsorption of the polymer to the nanoclay.

The XG adsorption was found do depend strongly on the hydration ability of counterions. The binding affinity of XG to Mnt was found to be strongest in the K-Mnt/XG system, followed by, in decreasing order, Na-Mnt/XG, Li-Mnt/XG, and Ca-Mnt/XG. The competing mechanism between ions, water and the XG in the interlayer region was shown to play an important role.

The dimensional stability upon moisture exposure, i.e. the ability of a material to resist swelling, is an important parameter for biopolymer-clay nanocomposites. While pure clay swells significantly even at low hydration levels, it is here shown that for the XG-Mnt system, at a hydration level below 50%, the inter-lamellar spacing is well preserved, suggesting a stable material performance. However, at higher hydration levels, the XG-Mnt composite was found to exhibit swelling at the same rate as the pure hydrated Mnt clay.

For the CHS-Mnt system, the significant electrostatic interactions from the direct charge-charge attraction between the polymer and the Mnt clay play a key role in the composite formation. Varying the degree of acetylation (DA) and the degree of protonation (DPr) resulted in different effects on the polymer-clay interaction. For the heavily acetylated CHS (DA > 50%, also known as chitin), the strong adhesion of the neutral chitin to the Mnt clay was attributed to strong correlation between the acetyl functional groups and the counterions which act as an electrostatic “glue”. Similarly, the poor adhesion of the fully deprotonated (DPr = 0%) neutral CHS to the clay is attributed to a weak correlation between the amino functional group and the counterions.

The stress-strain behavior of the CHS-Mnt composite shows that the mechanical properties are highly affected by the volume fraction of the Mnt clay and the degree of exfoliation of the composite. The material structure has a close relationship to the material properties.

Biopolymer-clay nanocomposites hold a bright future to replace petroleum-derived polymer plastics and will become widely used in common life. The theme of the thesis is that further critical improvements of these materials can be accomplished by development of the experimental methods in conjunction with increased understanding of the interactions between polymer, clay, water, ions, solutions in the polymer-clay mixtures provided by molecular modelling.

• 1179.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Stress-strain behavior in chitosan-montmorillonite nanocomposites studied by molecular dynamics simulationsManuscript (preprint) (Other academic)

We have performed molecular dynamics (MD) simulations to study the mechanical properties of bionanocomposites composed of chitosan (CHS) and montmorillonite (Mnt) clay. The stress-strain behavior and the Young’s modulus are calculated to estimate the mechanical properties of the material. Our results show that the mechanical properties of the CHS-Mnt composites are determined by many factors. The volume fraction and the degree of exfoliation of the clay platelets play the key roles. Meanwhile, the molecular adhesion between the polymer CHS and the Mnt at the wet interface is also a main factor. The stress-strain curve of the partially exfoliated CHS-Mnt composite shows significantly larger stiffness than the fully exfoliated one due to the volume fraction of clay is higher in the former case. The stiffness is slightly improved by adding more polymer in the fully exfoliated complex. We conclude that a higher volume faction of the Mnt is an essential premise to fabricate a high-performance composite material. The composite material structure has been found highly relevant to the mechanical properties. In addition, a strong molecular adhesion between the polymer and the clay would be of great importance for the mechanical properties in the composite material. The work provides insight into how to predict the mechanical properties in polymer-clay nanocomposites and may therefore be helpful for the design of bionanocomposite materials.

• 1180. Wang, Yan Alexander
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
Preface. Proceedings of the Sixth Congress of the International Society for Theoretical Chemical Physics2009In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 109, no 14, p. 3143-3144Article in journal (Other academic)
• 1181.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Hydration and dimensional stability of the intercalated galleries in xyloglucan/montmorillonite nanocomposites studied by molecular dynamics simulationsManuscript (preprint) (Other academic)

The outstanding properties of biological composite nacre materials have for a long time inspired research and development of man-made bionanocomposites. One of the most recent nacre-mimetic bionanocomposites comprising xygloglucan (XG) and montmorillonite (Mnt) clay has been investigated by related model systems through Molecular dynamics (MD) simulations. The expansion of the inter-gallery of the XG-Mnt composites when exposed to water, has been found to be a key issue for the material property. In order to shed light on the mechanism for this swelling behavior we have investigated the relation between the hydration and the dimensional stability of the inter-gallery in XG-Mnt composites, exploring also the role of the dynamic state of the polymer XG for the dimensional change. We find that at a hydration level below 50%, XG-Mnt possesses good dimensional stability, suggesting a constant performance of the material, while at a hydration level of 75%, the expansion ratio of the composite is found to be slightly smaller than the swelling of Mnt clay. At the four-layer hydrate formation with a hydration level of 100%, the swelling ratios of clay and the2composite reach the same value, suggesting a critical point of losing dimensional stability. We conclude that the strong adhesion between the polymer XG and the Mnt clay is the main driving force for the preservation of the stability at lower hydration conditions, while the dynamics of the XG polymer is related to the losing of dimensional stability for the composite at higher hydration levels. The ramification of these results in terms of moisture sensitivity of the material is briefly discussed.

• 1182.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Molecular mechanisms for the adhesion of chitin and chitosan to montmorillonite clayManuscript (preprint) (Other academic)

Molecular dynamics simulations have been performed to investigate molecular adhesion of chitin and chitosan oligomers to montmorillonite (Mnt) clay at different degrees of acetylation (DA, 0%, 20%, 40%, 60%, 80% and 100%) and different degree of protonation (DPr, 0%, 50%, 100% mimicking pH > 6.5, pH = 6.5, pH < 4, respectively) under fully hydrated conditions. Although the Mnt surface is negatively charged and a variation in DA also implies going from a positively charged oligomer at DA = 0% to a neutral oligomer at DA = 100%, the simulations show unexpectedly variation of the total molecular adhesion as a function of DA. From our analysis we propose that this quantitatively similar adhesion arise from two different mechanisms. At low DA, the oligomer is rich in positively charged amino groups interacting strongly with the negatively charged surface by direct electrostatic interaction. On the other hand, at high DA, electrically neutral acetyl groups are strongly correlated with the Na+ counter ions, which are in all cases stuck at the surface and the counter ions seem to act as ‘glue’ between the acetyl groups and the Mnt. However, when protonation was decreased, adhesion was significantly lowered. The reason is conclued by differences in charge distributions of the respective functional groups. A further investigation on the intramolecular hydrogen bonds formed in CHT or CHS shows that the adsorbed conformation of the polymer is also highly affected by DA. This work provides fundamental insights into adhesion mechanisms and is, of potential importance for the development of polymer-clay based composite materials.

• 1183.
KTH, School of Biotechnology (BIO).
Theoretical Design of Molecular Photonic Materials2007Doctoral thesis, comprehensive summary (Other scientific)

This thesis presents a theoretical study on optical properties of molecular materials. Special emphasis has been put on the influence of solvent environment, nuclear vibrations, and aggregation effects on molecular properties like linear and nonlinear polarizabilities, one- and two-photon absorption probabilities. All calculations have been performed by means of time independent and dependent quantum chemical methods at the Hartree-Fock and density functional theory levels. Solvation models that include both long range and short range interactions have been employed for calculations of optical properties of molecules in solutions. Pure vibrational and zero-point vibrationally averaged contributions have been taken into account for linear and nonlinear polarizabilities. The linear coupling model is applied to simulate vibronic profiles of optical absorption spectra. The computational strategies described in this thesis are very useful for the design of efficient molecular photonic materials.

More specifically, the nonmonotonic behavior of the solvatochromic shifts and the first hyperpolarizability of para-nitroaniline (pNA) with respect to the polarity of the solvents have been theoretically confirmed for the first time. The significant contributions of the hydrogen bonding on the electronic structures of pNA are revealed. Vibrational contributions to the linear and nonlinear polarizabilities of methanol, ethanol and propanol have been calculated both at the static limit and in dynamic optical processes. The importance of vibrational contributions to certain nonlinear optical processes have been demonstrated. A series of end-capped triply branched dendritic chromophores have been studied with the result that their second order nonlinear optical properties are found strongly dependent on the mutual orientations of the three chromophores, numbers of caps and the conjugation length of the chromophores. Several possible mechanisms for the origin of the Q-band splitting of aluminum phthalocyanine chloride have been examined. Calculated vibronic one-photon absorption profiles of two molecular systems are found to be in very good agreement with the corresponding experiments, allowing to provide proper assignments for different spectral features. Furthermore, effects of vibronic coupling in the nonradiative decay processes have been considered which helps to understand the aggregation enhanced luminescence of silole molecules. The study of molecular aggregation effects on two-photon absorption cross sections of octupolar molecules has highlighted the need to use a hybrid method that combines density functional response theory and molecular dynamics simulations for the design of molecular materials.

• 1184.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Department of Chemistry, University of Arizona. KTH, School of Biotechnology (BIO), Theoretical Chemistry. Department of Chemistry, University of Arizona. KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Solvent effects on the vibronic one-photon absorption profiles of dioxaborine heterocycles2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 19, p. 194311-1-194311-7Article in journal (Refereed)

The vibronic profiles of one-photon absorption spectra of dioxaborine heterocycles in gas phase and solution have been calculated at the Hartree-Fock and density-functional-theory levels. The polarizable continuum model has been applied to simulate the solvent effect, while the linear coupling model is used to compute the Franck-Condon and Herzberg-Teller contributions. It is found that a good agreement between theory and experiment can be achieved when the solvent effect and electron correlation are taken into account simultaneously. For the first excited charge-transfer state, the maximum of its Herzberg-Teller profile is blueshifted from that of the Franck-Condon profile. The shifted energy is found to be around 0.2 eV, which agrees well with the measured energy difference between two- and one-photon absorptions of the first excited state.

• 1185.
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
Hyperpolarizabilities of end-capped triply branched dendrimers: a theoretical studyIn: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690Article in journal (Other academic)
• 1186.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
KTH, School of Biotechnology (BIO), Theoretical Chemistry. KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Vibrational contributions to nonlinear optical properties of methanol, ethanol and propanol2005In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 717, no 1-3, p. 223-230Article in journal (Refereed)

Static and dynamic vibrational contributions to the linear polarizability and the first and second nonlinear hyperpolarizabilities of methanol, ethanol and propanol have been calculated. Both the pure vibrational contribution and the zero-point vibrational averaging contribution have been determined by adopting the perturbation treatment of Bishop and Kirtman at the Hartree-Fock level. The pure vibrational contribution is quite important at the static limit, while in the optical region it varies for different nonlinear optical processes. The zero-point vibrational averaging contribution is a quite large correction to the electronic nonlinear optical (NLO) properties, especially for the second hyperpolarizability at finite fundamental frequencies. Vibrational analysis shows that the swinging modes at around 300 cm(-1) and the C-H stretching modes at around 3160 cm(-1) often give large contributions.

• 1187.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Theoretical Studies on Artificial Water Splitting-Water Oxidation and Proton Transfer2012Licentiate thesis, comprehensive summary (Other academic)

The present thesis is concerned with the theoretical studies on artificial water splitting process. As the quick development of research on utilizing of solar energy, which is a green, clean, and renewable energy source, many research groups focus their attention on artificial photo-synthesis systems inspired by the photosystem I and II. The overall reaction in these artificial systems is water splitting to oxygen and hydrogen. Artificial water splitting can generally be divided into two half reactions, catalytic water oxidation and catalytic proton reduction. There is an increasing interest and demand to understand the detailed mechanism of these two key parts. Since DFT (density functional theory) in particular, has proven to be a powerful and popular tool in exploring reaction mechanisms, B3LYP and M06 functionals were employed to provide a theoretical explanation of these two important reactions in this thesis.

For water oxidation reaction, many efficient Water Oxidation Catalysts (WOCs) based on Ru, Ir, etc., have been reported over the last several years. The discovery of mononuclear ruthenium WOCs carrying anionic ligands is one of the major breakthroughs recently. WOCs bearing anionic ligands are able to efficiently drive catalytic water oxidation with relatively higher Turnover Numbers (TON) and Turnover Frequencies (TOF). Therefore the influence of anionic ligands gained our attention. We decided to carry out a detailed investigation on this effect, and try to propose a full mechanism of this catalytic water oxidation as well. We found that 1) The anionic ligands exert a promoting influence on the ligand exchange between picoline and water, which facilitates the formation of aqua-Ru complex, 2) The anionic ligands facilitate the complex access to higher oxidation states, which is necessary for the OO bond formation, and 3) The work of OO bond formation is in progress.

For the proton reduction reaction, the transport or movement of protons is vital and interesting in many biological and chemical processes, including the hydrogen uptake/production, the reduction of CO2 to formate, and the reduction of O2 to water. It is often related to energy storage and utilization. However, the details of these processes are still ambiguous. In most natural hydrogenase enzymes or synthetic catalysts based on iron or nickel, the incorporation of a pendant amine is a frequently occurring feature. This internal amine base seems to facilitate this proton transfer by acting as a proton relay. Our calculated results showed that the internal base allows for a splitting of one high enthalpy-high entropy barrier into two: one with a high enthalpy-low entropy barrier and the other with a low enthalpy-high entropy barrier, resulting in a low free energy of activation for proton transfer. Our results can serve as a guideline in the development of new catalysts, not only for proton reduction catalysts, but also for any process that involves proton transfer from a metal hydride to an external base, such as C-H activation and functionalization catalysts.

A thorough understanding on the mechanism of water splitting can help generate a strategy to enhance the catalytic performance on both water oxidation and proton reduction. We can tune or modify the synthetic complex by accelerating the slow step (rate-determining step) in the overall catalytic cycle, and can construct artificial water splitting systems with improved performance.

• 1188.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Theoretical Studies on Water Splitting Using Transition Metal Complexes2014Doctoral thesis, comprehensive summary (Other academic)
• 1189.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Theoretical study on H-2 activation on (FeFeI)-Fe-II complex 1(+)2014In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 248Article in journal (Other academic)
• 1190.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Theoretical Evidence for Direct Involvement of a Dissociated Picoline in Catalyst DecayManuscript (preprint) (Other academic)
• 1191. Wernet, Philippe
Stockholm University, Faculty of Science, Department of Physics.
Dissecting Local Atomic and Intermolecular Interactions of Transition-Metal Ions in Solution with Selective X-ray Spectroscopy2012In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 3, no 23, p. 3448-3453Article in journal (Refereed)

Determining covalent and charge-transfer contributions to bonding in solution has remained an experimental challenge. Here, the quenching of fluorescence decay channels as expressed in dips in the L-edge X-ray spectra of solvated 3d transition-metal ions and complexes was reported as a probe. With a full set of experimental and theoretical ab initio L-edge X-ray spectra of aqueous Cr3+, including resonant inelastic X-ray scattering, we address covalency and charge transfer for this prototypical transition-metal ion in solution. We dissect local atomic effects from intermolecular interactions and quantify X-ray optical effects. We find no evidence for the asserted ultrafast charge transfer to the solvent and show that the dips are readily explained by X-ray optical effects and local atomic state dependence of the fluorescence yield. Instead, we find, besides ionic interactions, a covalent contribution to the bonding in the aqueous complex of ligand-to-metal charge-transfer character

• 1192.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
PES Studies of Ru(dcbpyH2)2(NCS)2 Adsorption on Nanostructured ZnO for Solar Cell Applications2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 39, p. 10102-10107Article in journal (Refereed)

The interaction between the dye cis-bis(4,4‘-dicarboxy-2,2‘-bipyridine)-bis(isothiocyanato)-ruthenium(II), Ru(dcbpyH2)2(NCS)2, and nanostructured ZnO was investigated by photoelectron spectroscopy (PES) using synchrotron radiation. The results are compared with those of nanostructured TiO2 sensitized with the same dye, which to date is the most efficient system for dye-sensitized photoelectrochemical solar cells. When comparing the two metal oxides, differences in the surface molecular structure were observed both for low and high dye coverages, as seen by comparing the oxygen, nitrogen and sulfur signals. The origin of these differences is discussed in terms of substrate-induced dye aggregation and in variations in surface bonding geometries. The measurements also provide information concerning the energy matching between the orbitals of the dye and the ZnO valence band, which is of importance in photoinduced charge transfer.

• 1193.
Umeå University, Faculty of Science and Technology, Department of Chemistry.
A proton T1-nuclear magnetic resonance dispersion study of water motion in snowflakes and hexagonal ice2019In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 117, no 7-8, p. 960-967Article in journal (Refereed)

Snowflakes and ordinary hexagonal ice were studied measuring water proton spin–lattice relaxation rate R1(ωI)-nuclear magnetic resonance dispersion (NMRD) profiles at proton Larmor frequencies ranging from 1 to 30 MHz and at different temperatures ranging from −2◦C to −10◦C. The spin–spin relaxation rate 1/ 1/T2(ωI) was determined at a single Larmor frequency of 16.3 MHz. The high-field wing of the proton R1(ωI)-NMRD profile was characterised by two parameters: a correlation time τc which described the dipole–dipole spectral density, and the relaxation rate at low fields R max real (0) which was determined from T 2 . The correlation time τc depended on the dynamic model used. A rotation diffusion model yield approximatively 3μs at −3◦C to about 5μs at 10◦C, whereas for a more realistic six-site discrete exchange model, the correlation times decreased slightly to about 80% for the same temperature interval. Proton dipole–dipole interactions were divided into intramolecular and intermolecular contributions where the intermolecular contribution was about 0.4–0.8 × the intramolecular contribution. It was not possible to discriminate between the dynamic models or to detect ice/water interface effects by comparing the NMRD data from snowflakes with ordinary hexagonal ice data.

• 1194. Wheatley, James E.
Solvent promoted reversible cyclometalation in a tethered NHC iridium complex2014In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 50, no 6, p. 685-687Article in journal (Refereed)

Reaction of [Ir(COD)(py-(IBu)-Bu-t)](+) (py-(IBu)-Bu-t = 3-tert-butyl-1-picolylimidazol-2-ylidene) with acetonitrile results in reversible intramolecular C-H bond activation of the NHC ligand and formation of [Ir(g(2):g 1-C8H13)(py-ItBu’)(NCMe)](+). Coordinated COD acts as an internal hydride acceptor and acetonitrile coordination offsets the otherwise unfavourable thermodynamics of the process.

• 1195.
Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
Towards a synthetic avidin mimic2011In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 400, no 5, p. 1397-1404Article in journal (Refereed)

A series of streptavidin-mimicking molecularly imprinted polymers has been developed and evaluated for their biotin binding characteristics. A combination of molecular dynamics and NMR spectroscopy was used to examine potential polymer systems, in particular with the functional monomers methacrylic acid and 2-acrylamidopyridine. The synthesis of copolymers of ethylene dimethacrylate and one or both of these functional monomers was performed. A combination of radioligand binding studies and surface area analyses demonstrated the presence of selectivity in polymers prepared using methacrylic acid as the functional monomer. This was predicted by the molecular dynamics studies showing the power of this methodology as a prognostic tool for predicting the behavior of molecularly imprinted polymers.

• 1196.
Department of Pharmaceutical Chemistry, University of California, San Francisco.
Department of Pharmaceutical Chemistry, University of California, San Francisco. MS 239-4, Exobiology Branch, NASA Ames Research Center, Moffet Field, California. Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London. Department of Pharmaceutical Chemistry, University of California, San Francisco.
Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance2011In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 10, p. 2394-402Article in journal (Refereed)

Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K+ and Cl with their first solvation shells intact. The free energy barrier encountered by K+ is only 2.2 kcal/mol whereas Cl encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.

• 1197. Witzke, Sarah
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
An Averaged Polarizable Potential for Multiscale Modeling in Phospholipid Membranes2017In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 38, no 9, p. 601-611Article in journal (Refereed)

A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoylsn- glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids. Furthermore, the importance of explicit polarization is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural and dynamical studies.

• 1198.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
The range and shielding of dipole-dipole interactions in phospholipid bilayers2004In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 87, no 4, p. 2433-2445Article in journal (Refereed)

In molecular dynamics simulations of lipid bilayers, the structure is sensitive to the precise treatment of electrostatics. The dipole-dipole interactions between headgroup dipoles are not long-ranged, but the area per lipid and, through it, other properties of the bilayer are very sensitive to the detailed balance between the perpendicular and in-plane components of the headgroup dipoles. This is affected by the detailed properties of the cutoff scheme or if long-range interactions are included by Ewald or particle-mesh Ewald techniques. Interaction between the in-plane components of the headgroup dipoles is attractive and decays as the inverse sixth power of distance. The interaction is screened by the square of a dielectric permittivity close to the value for water. Interaction between the components perpendicular to the membrane plane is repulsive and decays as the inverse third power of distance. These interactions are screened by a dielectric permittivity of the order 10. Thus, despite the perpendicular components being much smaller in magnitude than the in-plane components, they will dominate the interaction energies at large distances.

• 1199.
Chalmers University of Technology, Gothenburg, Sweden.
Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; School of Science and Technology, Örebro University, Örebro, Sweden. University of Gothenburg, Gothenburg, Sweden. Örebro University, School of Science and Technology.
Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 818Article in journal (Refereed)

UVR8 (UV RESISTANCE LOCUS 8) is a UV-B photoreceptor responsible for initiating UV-B signalling in plants. UVR8 is a homodimer in its signalling inactive form. Upon absorption of UV radiation, the protein monomerizes into its photoactivated state. In the monomeric form, UVR8 binds the E3 ubiquitin ligase COP1 (CONSTITUTIVELY PHOTOMORPHOGENIC 1), triggering subsequent UV-B-dependent photomorphogenic development in plants. Recent in vivoexperiments have shown that the UVR8 C-terminal region (aa 397-423; UVR8C27) alone is sufficient to regulate the activity of COP1. In this work, CD spectroscopy and NMR experiments showed that the UVR8C27domain was non-structured but gained secondary structure at higher temperatures leading to increased order. Bias-exchange metadynamics simulations were also performed to evaluate the free energy landscape of UVR8C27. An inverted free energy landscape was revealed, with a disordered structure in the global energy minimum. Flanking the global energy minimum, more structured states were found at higher energies. Furthermore, stabilization of the low energy disordered state was attributed to a proline residue, P411, as evident from P411A mutant data. P411 is also a key residue in UVR8 binding to COP1. UVR8C27is therefore structurally competent to function as a molecular switch for interaction of UVR8 with different binding partners since at higher free energies different structural conformations are being induced in this peptide. P411 has a key role for this function.

• 1200.
University of Gothenburg, Gothenburg, Sweden.
Örebro University, School of Science and Technology. University of Gothenburg, Gothenburg, Sweden.
Prediction of the thre-dimensional structure of the plant UVR8 photoreceptor dimer, and the key residues in UV-B regulated signalling pathway2012In: Science and Technology Day 2012.: Poster exhibition, 2012, p. C28-C28Conference paper (Other academic)

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