Elektroninio sužadinimo evoliucija šviesai jautriose molekulėse yra reiškinys, kuriuo remiantis įmanoma nagrinėti daugelį natūralių ir dirbtinių procesų: augalų ir bakterijų fotosintezę, regos mechanizmą, optomechaninių bei optoelektroninių prietaisų (pavyzdžiui, organinių šviestukų) veikimą. Teoriškai šis reiškinys modeliuojamas sprendžiant laikinę Šriodingerio lygtį. Deja, toks sprendimas realiems, praktiškai panaudojamiems junginiams šiandien yra per sudėtingas uždavinys, todėl jį tenka keisti supaprastinant nagrinėjamų junginių modelius arba sprendimo metodiką. Šioje disertacijoje aprašomų tyrimų tikslas buvo elektroninės struktūros skaičiavimų metodais (t. y. sprendžiant paprastesnę nuostoviąją Šriodingerio lygtį) ištirti elektroninio sužadinimo sukeltus procesus fotoaktyviose molekulėse ir sudaryti sužadinimo relaksaciją apibūdinančius potencinės energijos paviršių modelius. Parodoma, jog ta pačia metodika atliekamų tyrimų rezultatai paaiškina įvairiuose junginiuose vykstančius reiškinius: bakteriorodopsino baltymo funkcinės grupės vykdomą protono pernašą poliniame tirpiklyje, indolo-benzoksazino junginio optomechaninį ciklą, našią fosforescenciją organiniame silicio polimere bei šviestukams naudojamo metaloorganinio komplekso su prijungtomis krūvininkų pernašos grupėmis ypatybes. / Evolution of the electronic excitation is a general process that can be used to explain many natural and artificial phenomena, such as photosynthesis in plants and bacteria, biological mechanism of vision, and operating principles of optomechanical and optoelectronic devices. This process is theoretically modeled by solving the time-dependent Schroedinger equation. However, such treatment is too computationally expensive to be used for practical molecular systems. Therefore, either models of the structure of the systems or the solving procedure itself must be simplified to get the desired results. The main goal of the research presented in this dissertation was to study processes caused by the electronic excitation in photoactive molecules using computational methods of electronic structure (i. e. solving the simpler time-independent Schroedinger equation) and to construct the potential energy surface models describing the energy relaxation in the investigated molecules. It is shown that the results of different investigations performed using the same procedure provide explanations of different phenomena in various compounds, such as: proton transfer in polar solvent, performed by a functional group of the bacteriorhodopsin protein; optomechanical cycle of the indolo-benzoxazine compound; efficient phosphorescence of the silicon-based organic polymer; and optical properties of organometallic emitter compound with additional charge-carrier groups.

Evolution of the electronic excitation is a general process that can be used to explain many natural and artificial phenomena, such as photosynthesis in plants and bacteria, biological mechanism of vision, and operating principles of optomechanical and optoelectronic devices. This process is theoretically modeled by solving the time-dependent Schroedinger equation. However, such treatment is too computationally expensive to be used for practical molecular systems. Therefore, either models of the structure of the systems or the solving procedure itself must be simplified to get the desired results. The main goal of the research presented in this dissertation was to study processes caused by the electronic excitation in photoactive molecules using computational methods of electronic structure (i. e. solving the simpler time-independent Schroedinger equation) and to construct the potential energy surface models describing the energy relaxation in the investigated molecules. It is shown that the results of different investigations performed using the same procedure provide explanations of different phenomena in various compounds, such as: proton transfer in polar solvent, performed by a functional group of the bacteriorhodopsin protein; optomechanical cycle of the indolo-benzoxazine compound; efficient phosphorescence of the silicon-based organic polymer; and optical properties of organometallic emitter compound with additional charge-carrier groups. / Elektroninio sužadinimo evoliucija šviesai jautriose molekulėse yra reiškinys, kuriuo remiantis įmanoma nagrinėti daugelį natūralių ir dirbtinių procesų: augalų ir bakterijų fotosintezę, regos mechanizmą, optomechaninių bei optoelektroninių prietaisų (pavyzdžiui, organinių šviestukų) veikimą. Teoriškai šis reiškinys modeliuojamas sprendžiant laikinę Šriodingerio lygtį. Deja, toks sprendimas realiems, praktiškai panaudojamiems junginiams šiandien yra per sudėtingas uždavinys, todėl jį tenka keisti supaprastinant nagrinėjamų junginių modelius arba sprendimo metodiką. Šioje disertacijoje aprašomų tyrimų tikslas buvo elektroninės struktūros skaičiavimų metodais (t. y. sprendžiant paprastesnę nuostoviąją Šriodingerio lygtį) ištirti elektroninio sužadinimo sukeltus procesus fotoaktyviose molekulėse ir sudaryti sužadinimo relaksaciją apibūdinančius potencinės energijos paviršių modelius. Parodoma, jog ta pačia metodika atliekamų tyrimų rezultatai paaiškina įvairiuose junginiuose vykstančius reiškinius: bakteriorodopsino baltymo funkcinės grupės vykdomą protono pernašą poliniame tirpiklyje, indolo-benzoksazino junginio optomechaninį ciklą, našią fosforescenciją organiniame silicio polimere bei šviestukams naudojamo metaloorganinio komplekso su prijungtomis krūvininkų pernašos grupėmis ypatybes.

The electronic and geometrical structure of single difluoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene (aza-BODIPY) molecules adsorbed on the Au(111) surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with ab initio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-BODIPY molecule forms a chemical bond with the Au(111) substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of 1 V. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Metastable (Ti,Si)N alloy and TiN/SiNx multilayer thin solid films as well as SiNx/TiN surfaces have been explored. Cubic Ti1-xSixN (0≤x≤0.14) films deposited onto cemented carbide (WC-Co) substrates by arc evaporation exhibited a competitive columnar growth mode where the structure transforms to a feather-like nanostructure with increasing Si content as revealed by x-ray diffraction and transmission electron microscopy. X-ray photoelectron spectroscopy revealed the presence of Ti-N and Si-N bonding, but no amorphous Si3N4. Band structure calculations showed that phase separation of NaClstructure Ti1-xSixN solid solution into cubic SiN and TiN phases is energetically favorable. The metastable microstructure, however, was maintained for the Ti0.86Si0.14N film annealed at 900°C, while recrystallization in the cubic state took place at 1100°C annealing during 2h. The Si content influenced the film hardness close to linearly, by combination of solid-solution hardening in the cubic state and defect hardening. For x=0 and x=0.14, nanoindentation gave a hardness of 29.9±3.4 GPa and 44.7±1.9 GPa, respectively. The hardness was retained during annealing at 900°C. Nanostructured materials, e.g., nanocomposites and nanolaminates, are defined by internal interfaces, of which the nature is still under debate. In this work two-phase model systems were explored by depositing SiNx/TiN nanolaminate films, including superlattices containing cubic SiNx, by dual target reactive magnetron sputtering. It is demonstrated that the interfacial phase of SiNx onto TiN(001) and TiN(111) can be crystalline, and even epitaxial with complex surface reconstructions. Using in situ structural analyses combined with ab initio calculations, it is found that SiNx layers grow epitaxially, giving rise to strong interfacial bonding, on both TiN(001) and TiN(111) surfaces. In addition, TiN overlayers grow epitaxially on SiNx/TiN(001) bilayers in nanolaminate structures. These results provide insight into the development of design rules for novel nanostructured materials. / Report code: LiU-TEK-LIC-2006:51.

Computer modeling of enzymes is a valuable complement to experiments. Quantum chemical studies of enzymatic reactions can provide a detailed description of the reaction mechanism and elucidate the roles of various residues in the active site. Different reaction pathways can be analyzed, and their feasibility be established based on calculated energy barriers. In the present thesis, density functional theory has been used to study the active sites and reaction mechanisms of three different enzymes, cytosine deaminase (CDA) from Escherichia coli, ω-transaminase from Chromobacterium violaceum (Cv-ωTA) and dinitrogenase reductase-activating glycohydrolase (DraG) from Rhodospirillum rubrum. The cluster approach has been employed to design models of the active sites based on available crystal structures. The geometries and energies of transition states and intermediates along various reaction pathways have been calculated, and used to construct the energy graphs of the reactions. In the study of CDA (Paper I), two different tautomers of a histidine residue were considered. The obtained reaction mechanism was found to support the main features of the previously proposed mechanism. The sequence of the events was established, and the residues needed for the proton transfer steps were elucidated. In the study of Cv-ωTA (Paper II and Paper III), two active site models were employed to study the conversion of two different substrates, a hydrophobic amine and an amino acid. Differences and similarities in the reaction mechanisms of the two substrates were established, and the role of an arginine residue in the dual substrate recognition was confirmed. In the study of DraG (Paper IV), two different substrate-binding modes and two different protonation states of an aspartate residue were considered. The coordination of the first-shell ligands and the substrate to the two manganese ions in the active site was characterized, and a possible proton donor in the first step of the proposed reaction mechanism was identified. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

A coupling-limited approach for the Ullmann reaction-like on-surface synthesis of a two-dimensional covalent organic network starting from a halogenated metallo-porphyrin is demonstrated. Copper-octabromo-tetraphenylporphyrin molecules can diffuse and self-assemble when adsorbed on the inert Au(111) surface. Splitting-off of bromine atoms bonded at the macrocyclic core of the porphyrin starts at room temperature after the deposition and is monitored by X-ray photoelectron spectroscopy for different annealing steps. Direct coupling between the reactive carbon sites of the molecules is, however, hindered by the molecular shape. This leads initially to an ordered non-covalently interconnected supramolecular structure. Further heating to 300 °C and an additional hydrogen dissociation step is required to link the molecular macrocycles via a phenyl group and form large ordered polymeric networks. This approach leads to a close-packed covalently bonded network of overall good quality. The structures are characterized using scanning tunneling microscopy. Different kinds of lattice defects and, furthermore, the impact of polymerization on the HOMO–LUMO gap are discussed. Density functional theory calculations corroborate the interpretations and give further insight into the adsorption of the debrominated molecule on the surface and the geometry and coupling reaction of the polymeric structure. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

An understanding of the fundamental mechanism behind the relief of shear stress in single-crystal silicon subject to loading by shock-waves has to this day remained elusive. What is known is that this material undergoes a first-order pressure-induced polymorphic phase transition from its ambient pressure cubic-diamond (cd) crystal structure to its first stable high-pressure phase, known as &beta;-Sn, at a pressure of about 120 kbar under hydrostatic compression. By investigating the evolution of the transition parameters for this phase transition as a function of increasing uniaxial shear stress representative of the effects of shock-compression via ab-initio Density Functional Theory computational techniques, we predict a significant lowering of the stress at which the phase transition occurs. This raises the question as to whether the onset of plastic response at the material's Hugoniot Elastic Limit (HEL) reported in experiments corresponds in fact to the phase transition itself, a very plausible possibility which has never been considered before. Furthermore, we present molecular dynamics simulations using a Tersoff-like potential of shock-compressed single crystals of silicon. We find an elastic response up to a critical stress, above which the shear stress is relieved by an inelastic response associated with a partial transformation to a new high-pressure phase, where both the new phase (Imma) and the original cubic diamond phase are under close to hydrostatic conditions. We note that these simulations are also consistent with shear stress relief provided directly by the shock-induced phase transition itself, without an intermediate state of plastic deformation of the cubic diamond phase.

Ground state destabilization is a hypothesis to explain enzyme catalysis. The most popular interpretation of it is the entropic effect, which states that enzymes accelerate biochemical reactions by bringing the reactants to a favorable position and orientation and the entropy cost of this is compensated by enthalpy of binding. Once the enzyme-substrate complex is formed, the reaction could proceed with negligible entropy cost. Deamination of cytidine catalyzed by E.coli cytidine deaminase appears to agree with this hypothesis. In this reaction, the chemical transformation occurs with a negligible entropy cost and the initial binding occurs with a large entropy penalty that is comparable to the entropic cost of the uncatalyzed reaction. Our calculations revealed that this reaction occurs with different mechanisms in the cytidine deaminase and water. The uncatalyzed reaction involves a concerted mechanism and the entropy cost of this reaction appears to be dominated by the reacting fragments and first solvation shell. The catalyzed reaction occurs via a stepwise mechanism in which a hydroxide ion acts as the nucleophile. In the active site, the entropy cost of hydroxide ion formation is eliminated due to pre-organization of the active site. Hence, the entropic effect in this reaction is due to a pre-organized active site rather than ground state destabilization. In the second part of this thesis, we investigated peptide bond formation and peptidyl-tRNA hydrolysis at the peptidyl transferase center of the ribosome. Peptidyl-tRNA hydrolysis occurs by nucleophilic attack of a water molecule on the ester carbon of peptidyl-tRNA. Our calculations showed that this reaction proceeds via a base catalyzed mechanism where the A76 O2’ is the general base and activates the nucleophilic water. Peptide bond formation occurs by nucleophilic attack of the α-amino group of aminoacyl-tRNA on the ester carbon of peptidyl-tRNA. For this reaction we investigated two mechanisms: i) the previously proposed proton shuttle mechanism which involves a zwitterionic tetrahedral intermediate, and ii) a general base mechanism that proceeds via a negatively charged tetrahedral intermediate. Although both mechanisms resulted in reasonable activation energies, only the proton shuttle mechanism found to be consistent with the pH dependence of peptide bond formation.

Downscaling of the contact length Lc of a side-contacted carbon nanotube field-effect transistor (CNTFET) is challenging because of the rapidly increasing contact resistance as Lc falls below 20–50 nm. If in agreement with existing experimental results, theoretical work might answer the question, which metals yield the lowest CNT–metal contact resistance and what physical mechanisms govern the geometry dependence of the contact resistance. However, at the scale of 10 nm, parameter-free models of electron transport become computationally prohibitively expensive. In our work we used a dedicated combination of the Green function formalism and density functional theory to perform an overall ab initio simulation of extended CNT–metal contacts of an arbitrary length (including infinite), a previously not achievable level of simulations. We provide a systematic and comprehensive discussion of metal–CNT contact properties as a function of the metal type and the contact length. We have found and been able to explain very uncommon relations between chemical, physical and electrical properties observed in CNT–metal contacts. The calculated electrical characteristics are in reasonable quantitative agreement and exhibit similar trends as the latest experimental data in terms of: (i) contact resistance for Lc = ∞, (ii) scaling of contact resistance Rc(Lc); (iii) metal-defined polarity of a CNTFET. Our results can guide technology development and contact material selection for downscaling the length of side-contacts below 10 nm.

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