In this thesis I concentrate on the description of electron transport properties of microscopic objects, including molecular junctions and nano junctions, in particular, inelastic electron tunneling in surface-adsorbate systems are examined with more contemplations. Boosted by the rapid advance in experimental techniques at the microscopic scale, various electric experiments and measurements sprung up in the last decade. Electric devices, such as transistors, switches, wires, etc. are expected to be integrated into circuit and performing like traditional semiconductor integrated circuit (IC). On the other hand, detailed information about transport properties also provides new physical observable quantities to characterize the systems. For molecular electronics, which is in the state of growing up, its further applications demands more thorough understanding of the underlying mechanism, for instance, the effects of molecular configuration and conformation, inter- or intra-molecular interactions, molecular-substrate interactions, and so on. Inelastic electron tunneling spectroscopy (IETS), which reflects vibration features of the system, is also a finger print property, and can thus be employed to afford the responsibility of single molecular identification with the help of other experimental techniques and theoretical simulations.There are two parts of work presented in this thesis, the first one is devoted to the calculation of electron transport properties of molecular or nano junctions: we have designed a negative differential resistance (NDR) device based on graphene nanoribbons (GNRs), where the latter is a star material in scientific committee since its birth;The transport properties of DNA base-pair junctions are also examined by theoretical calculation, relevant experimental results on DNA sequencing have been explained and detailed issues are suggested.The second part focused on the simulation of scanning tunneling microscope mediated IETS (STM-IETS). We have implemented a numerical scheme to calculate the inelastic tunneling intensity based on Tersoff-Hamann approximation and finite difference method, benchmark results agree well with experimental and previous theoretical ones; Two applications of single molecular chemical identification are also presented following benchmarking. / QC20100630

Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms. The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions. Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.

Oscillator strengths and transition energies are calculated for several mono-substitutes of benzene and naphthalene molecules. The substituents investigated are chlorine, bromine and iodine. Calculations for these molecules are presented, at the Hartree-Fock and DFT level of theory. The functional used in DFT is CAM-B3LYP.

<p>Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. </p><p>The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.</p><p>The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-<i>Z,syn</i> configuration (in the inactive form of the protein) to C15-<i>E,anti</i> (in the active form). In this work, a reaction mechanism for this isomerization is proposed. </p><p>DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.</p><p>Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.</p>

Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work. The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed. DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied. Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.

<p>In dye-sensitized solar cells, the functions of light absorption and charge transport are separated. A photosensitive ruthenium-polypyridine dye in the cell absorbs light, injects an electron to a semiconductor and is then regenerated by a redox couple, typically iodide/triiodide. Quantum chemical calculations of the electronic structure of triiodide have been carried out with the restricted active space SCF method, including spin-orbit coupling, and with density functional theory. It was shown that the difference in charge density between the terminal and central atoms results in a splitting of the core levels. The calculations gave a value of the splitting of 0.8 - 1.0 eV for the <em>3d</em> and <em>4d</em> levels. Experimentally, the electronic structure has been investigated with photoelectronspectroscopy. The measured terminal/center splitting is 1.1 eV.The spin-orbit interaction of the <em>4d </em>levels of triiodide has also been calculated. The splitting was determined to be 1.6 eV. The experimental value is 1.7 eV. An assignment of the peaks in the computed spectrum of triiodide was made and the features of the experimental spectrum have beenidentied.The theoretical valence spectrum of triiodide has been computed and assigned. The results can be used in the analysis of photoelectron spectra of the molecule. Information about the electronic structure of the redox couple can help in the understanding of the electron transfer processes and forfurther development of the solar cells.  Furthermore, the solvation structure of the prototype dye, the tris(bipyridine)ruthenium(II) complex, in water and its interaction with iodide and chloride has been studied by means of molecular dynamics simulations. The trajectory analysis showed that the water molecules in the first solvation shell form a chain in between the bipyridine ligands. It was found that the iodide ions are more likely than chloride to enter between the ligands, which can be important for the electron transfer processin the solar cell.</p>

In dye-sensitized solar cells, the functions of light absorption and charge transport are separated. A photosensitive ruthenium-polypyridine dye in the cell absorbs light, injects an electron to a semiconductor and is then regenerated by a redox couple, typically iodide/triiodide. Quantum chemical calculations of the electronic structure of triiodide have been carried out with the restricted active space SCF method, including spin-orbit coupling, and with density functional theory. It was shown that the difference in charge density between the terminal and central atoms results in a splitting of the core levels. The calculations gave a value of the splitting of 0.8 - 1.0 eV for the 3d and 4d levels. Experimentally, the electronic structure has been investigated with photoelectronspectroscopy. The measured terminal/center splitting is 1.1 eV.The spin-orbit interaction of the 4d levels of triiodide has also been calculated. The splitting was determined to be 1.6 eV. The experimental value is 1.7 eV. An assignment of the peaks in the computed spectrum of triiodide was made and the features of the experimental spectrum have beenidentied.The theoretical valence spectrum of triiodide has been computed and assigned. The results can be used in the analysis of photoelectron spectra of the molecule. Information about the electronic structure of the redox couple can help in the understanding of the electron transfer processes and forfurther development of the solar cells.  Furthermore, the solvation structure of the prototype dye, the tris(bipyridine)ruthenium(II) complex, in water and its interaction with iodide and chloride has been studied by means of molecular dynamics simulations. The trajectory analysis showed that the water molecules in the first solvation shell form a chain in between the bipyridine ligands. It was found that the iodide ions are more likely than chloride to enter between the ligands, which can be important for the electron transfer processin the solar cell.

Physisorption of CO and N2O on surfaces of ceria (CeO2) was investigated by means of high-level quantum-mechanical embedded cluster calculations. Both systems have high relevance in the field of environmental chemistry and heterogeneous catalysis. The CO/CeO2 system, has been investigated in a couple of both experimental and theoretical studies, but for the N2O/CeO2 system, this is the first study in the literature, experimental or theoretical. In physisorption, the interaction relies entirely on classical electrostatic interactions and electron dispersion forces. No covalent bond is formed between the molecule and the surface. A proper description of the dispersion requires some of the most accurate quantum-mechanical methods available, such as MP2 or CCSD(T). Moreover, even the most sophisticated methods cannot heal errors anywhere else in the theoretical treatment. Standard periodic models cannot be used with methods such as CCSD(T), but embedded cluster models can, and have been thoroughly explored in this thesis. In this thesis, embedded cluster models were constructed for the CeO2(110) and (111) surfaces. Using a range of assessment tests, it was verified that the electronic structure of the central region of a large and fully embedded surface cluster agrees well with the corresponding region in a periodic system. CO physisorption was investigated at the CCSD(T) level. Due to the prohibitively large expenses (in computer time) for standard CCSD(T) calculations, the method of increments, previously used in the literature for bulk systems, was extended to adsorption problems. It was found that, electron correlation contributes by 30 - 80% to the molecule-surface interaction and that the contribution depends on the topology of the surface. The calculated CO-ceria interaction energy is 20 kJ/mol for the (111) surface and 27 kJ/mol for the (110) surface. In low temperature TPD experiments for the N2O/CeO2(111) system, one surface species was found with an adsorption energy of about 29 kJ/mol. IR measurements showed stretching frequencies that are typically assigned to N2O adsorption with the O-end directed towards surface cations. However, theoretical calculations up to the MP2 level predicted two equally favorable adsorption species. Improvements in the structural model (larger clusters, consideration of molecule-induced relaxation) or the computational method (larger basis sets) did not affect this result. Only at the CCSD(T) level was one dominating surface species found, namely N2O adsorbed over a Ce ion, with the O-end of the molecule directed towards the surface. The calculated stretching vibrational frequency shifts (with respect to the gas phase) for this adsorbed species agree well with the measured IR spectra.

Interfaces between semiconductors and adsorbed molecules form a central area of research in surface science, occurring in many different contexts. One such application is the so-called Dye-Sensitized Solar Cell (DSSC) where the nanostructured dye-semiconductor interface is of special interest, as this is where the most important ultrafast electron transfer process takes place. In this thesis, structural and electronic aspects of these interfaces have been studied theoretically using quantum chemical computations applied to realistic dye-semiconductor systems. Periodic boundary conditions and large cluster models have been employed together with hybrid HF-DFT functionals in the modeling of nanostructured titanium dioxide. A study of the adsorption of a pyridine molecule via phosphonic and carboxylic acid anchor groups to an anatase (101) surface showed that the choice of anchor group affects the strength of the bindings as well as the electronic interaction at the dye-TiO2 interface. The calculated interfacial electronic coupling was found to be stronger for carboxylic acid than for phosphonic acid, while phosphonic acid binds significantly stronger than carboxylic acid to the TiO2 surface. Atomistic and electronic structure of realistic dye-semiconductor interfaces were reported for RuII-bis-terpyridine dyes on a large anatase TiO2 cluster and perylene dyes on a periodic rutile (110) TiO2 surface. The results show strong influence of anchor and inserted spacer groups on adsorption and electronic properties. Also in these cases, the phosphonic acid anchor group was found to bind the dyes significantly stronger to the surface than the carboxylic acid anchor, while the interfacial electronic coupling was stronger for the carboxylic anchor. The estimated electron injection times were twice as fast for the carboxylic anchor compared to the phosphonic anchor. Moreover, the electronic coupling was affected by the choice of spacer group, where unsaturated spacer groups were found to mediate electron transfer more efficiently than saturated ones.

Detta projekt fokuserar på att undersöka dynamiken hos partiklar inom en-partikelsystem samt sammankopplade partiklar i tvåpartikelsystem genom tillämpning av numeriska metoder. Tvåpartikelsystemet som studeras är NaI-molekylen och dess dynamik, där beteendet undersöks efter systemet utsatts för en femtosekundslaserpuls. För att uppnå projektets mål utformas numeriska metoder med hjälp av finita differenser och Arnoldis tidsintegrationsalgoritm samt Runge-Kutta 4. Metoderna utvärderas med hjälp av den kvantharmoniska oscillatorn som har en analytisk lösning. Konvergensen för de olika ordningarnas finita differenser testas på den tidsoberoende Schrödingerekvationen för systemet. Arnoldi och RK 4 utvärderas på den tidsberoende Schrödingerekvationen. Baserat på dessa resultat görs en tidkonvergens- och tidseffektivitetsanalys för tidsstegningssmetoderna. Studien visar på att Arnoldi-metoden uppvisar ett större stabilitetsområde, vidare visas det att RK4 är den mindre beräkningstunga metoden för den kvantharmoniska oscillatorn. Resultatet av förstudien visar att finita differenser av åttonde ordningen ger den mest noggranna numeriska approximationen, utöver det görs avvägningen att tidsstegningsmetoderna kräver ytterligare undersökning. Därefter tillämpas den numeriska metoden för att analysera dynamiken hos NaI-molekylen. Tidseffektivitetsstudien för denna del av projektet visar att Arnoldi med 10 iterationer är mest passande för resten av projektet på grund av dess stabilitetsområde samt fördelaktiga hantering av större mer komplexa Hamiltonianer. Simuleringarna av tvåpartikelsystemet visar att när laserns våglängd varierar, varierar den energimängd som tillförs till systemet. Detta kan ses i att populationsnivån på den övre potentialytan är högre för kortare våglängder, och även i att perioden för oscillationerna är längre. När varaktigheten hos laserpulsen ökas observeras en större population på den högre energinivån. Detta eftersom en lång pulslängd leder till en minskad variation i population av energinivåerna på de exciterade vågfunktionerna. För laserpulser vars våglängd korresponderar med rätt energi för excitation leder det till en högre population av exciterade vågfunktioner. Projektets resultat bidrar till en djupare grundläggande förståelse av hur olika parametrar hos femtosekundslasrar påverkar kemiska reaktioner och dynamik på submolekylär nivå.