The aim of this thesis was to investigate carbon based molecular materials at first principles levels. Special attention has been paid to simulations of X-ray spectroscopies, including near edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron, and X-ray emission spectroscopy, which can provide detailed information about core, occupied and unoccupied molecular orbitals of the systems under investigation. Theoretical calculations have helped to assign fine spectral structures in high resolution NEXAFS spectra of five azabenzenes (pyridine, pyrazine, pyrimidine, pyridazine and s-triazine), and to identify different local chemical environments among them. With the help of NEXAFS, the characters of important chemical bonds that might be responsible for the unique magnetic properties of the tetracyanoethylene compound has been revealed. Calculations have demonstrated that X-ray spectroscopies are powerful tools for isomer identification and structure determination of fullerenes and endohedral metallofullerenes. A joint experimental and theoretical study on metallofullerene Gd@C82 has firmly determined its equilibrium structure, in which the gadolinium atom lies above the hexagon on the C2 axis. It is found that the gadolinium atom could oscillate around its equilibrium position and that its oscillation amplitude increases with increasing temperature. In this thesis, several new computational schemes for large-scale systems have been proposed. Parallel implementation of a central insertion scheme (CIS) has been realized, which allows to effectively calculate electronic structures of very large systems, up to 150,000 electrons, at hybrid density functional theory levels. In comparison with traditional computational methods, CIS provides results with the same high accuracy but requires only a fraction of computational time. One of its applications is to calculate electronic structures of nanodiamond clusters varying from 0.76 nm (29 carbons) to 7.3 nm (20,959 carbons) in diameter, which enabled to resolve the long-standing debate about the validity of the quantum confinement model for nanodiamonds. Electronic structures and X-ray spectroscopies of a series of single-walled carbon nanotubes (SWCNTs) with different diameters and lengths have been calculated, which have made it possible to interpret the existing experimental results. / QC 20100727

Lignins are produced by all vascular plants and they represent one of the most abundant groups of biopolymers in nature. Lignin chemistry research, which has been of great importance for the progress of pulping technologies, has been plagued by the difficulties of its isolation and characterization. The pioneering work of Karl Freudenberg in the 1950’s with synthetic models of lignin paved the way for a detailed structural characterization of many lignin substructures. His work with the so-called “synthetic lignins” or dehydrogenative polymers (DHP) also laid a foundation for understanding how different lignin substructures are formed, reinforcing the already existing theory of lignin polymerization. However, subsequent structural characterizations of DHPs and lignins have repeatedly put this theory to the test. In the past decade, even a new radically different hypothesis for lignin polymerization has emerged and is sustained by a few researchers in the field. In this work, DHPs were produced from phenolic monomers, mostly coniferyl alcohol, a common lignin monomer, in a variety of reaction conditions. This was done in order to establish how different chemical factors, potentially active in the plant cell wall during lignin polymerization, influence the polymer’s final properties. In the presence of nicotine amide adenine dinucleotide (NADH), a quinone methide model, which is an intermediate formed during lignin polymerization, was effectively reduced. An equivalent reduced structure was produced during DHP synthesis in the presence of NADH. These studies showed that reduction might take place during oxidative polymerization, possibly explaining how reduced lignin structures are formed in the plant cell wall. Another reductive agent, ascorbic acid, was also tested during synthesis of DHPs. It displayed a totally different effect than NADH, probably due to its anti-oxidant nature, by altering the final amounts of certain inter-unit substructures, in favour of β-O-4′ structures, which are so prominent in natural lignins. Furthermore, the new suggested model for lignin polymerization, stating that lignin itself possesses the ability for template replication, was tested by synthesizing DHPs in the presence of a simple β-β′ substructure model. The DHPs produced the same amounts of β-β′ substructures as a control synthesis without the model structure, indicating that no replication had occurred. Finally, the role of the monolignol γ-carbon oxidation state in lignin polymerization, was studied. Hypothetically, lignin- like polymers could be produced by the plant, using monolignol biosynthetic precursors which exhibit γ-carbonyl groups instead of an alcohol group, like the common lignin monomer. Synthetic lignins produced with ferulic acid, coniferaldehyde and the normal monolignol, coniferyl alcohol, displayed important differences in chemical and physical properties. Both the ferulic acid and coniferaldehyde polymers exhibited almost no saturated inter-unit substructures and very few cyclic structures, both of which are very common in coniferyl alcohol dehydrogenative polymers and natural lignins. This could have significant implications for the formation of an important type of lignin carbohydrate complexes (LCC). Also the hydrophobicity of the alcohol-type polymer was lower than the other two. The biological implications of all these findings are discussed and some suggestions are made to explain how all these factors might affect lignin polymerization and structure in nature. / QC 20100811

During the last decade, the dye sensitised solar cell (DSC) has attracted much attention. The technology has a potential to act as a new generation of photovoltaic device, it has also increased our knowledge within the field of photoelectrochemistry. The materials used in the DSC have been used in other technologies, such as electrochromic displays. This thesis examines how such systems can be analysed to understand their properties from their components. Both of the considered device technologies consist of a thin mesoporous semiconductor film immersed in an electrolyte. The study starts by investigating some of the fundamental properties of the mesoporous semiconductor and its interface with the electrolyte. This gives rise to the charge-voltage relationship for the devices, which is related to the chemical capacitance and electronic energy levels for the materials. In particular,special attention is given to the DSC and the properties of the charge carriers in the semiconductor. For the DSC, several techniques have been developed in order to understand the processes of transport and recombination for the charge carriers in the semiconductor film, which are vitally important for performance. In this thesis, particular focus is given to light modulation techniques and electrical analysis with impedance spectroscopy. The transportproperties show for both techniques a nonlinear behaviour, which is explained with the trapping model. The DSC solar cell is analysed in order to interpret the transport measurements for film thickness optimisation. DSC cells with new semiconductor materials, such as ZnO, were analysed with impedance measurements to provide new insights into the optimisation of the performance of the photoelectrochemical solar cell technology. / QC 20100804

Den kopparbindande egenskapen hos prionproteiner är sannolikt kopplad till proteinets funtion. Det mänskliga prionproteinet innehåller ett kopparbindande oktapeptidområde, där PHGGGWGQ-sekvensen upprepas fyra gånger i följd. Syftet med detta arbete är att undersöka strukturen och dynamiken i oktapeptidområdet genom att använda teoretiska metoder. Med kvantkemisk strukturoptimering genomfördes en detaljerad jämförelse av växelverkan mellan flera katjoner och det kopparbindande området. Enligt dessa beräkningar är rodium(III) en möjlig ersättare för koppar(II) i NMR-specktroskopiska koordinationsstudier. Alternativa solvatiseringsmodeller i molekyldynamiksimuleringar har också jämförts. Periodiska randvillkor är mest lämpade för användning i de system som undersöks i detta arbete. Molekyldynamiksimuleringar användes för att jämföra oktapeptidområdets struktur och dynamik med och utan kopparjoner. Växelverkan mellan aminosyrornas ringar påverkar starkt strukturen i detta område i frånvaro av kopparjoner. Fyra olika icke-bindande och bindande modeller har studerats, vilka skiljer i sin beskrivning av växelverkan mellan koppar och proteinet. Teoretiska EXAFS spektra beräknades från dem simulerade strukturerna. Spektra som genererats för den bindande modellen är nästan identiska med experimentiella resultat, vilket stöder användandet av den bindande modellen. Detta arbete visar att kopparjoner interagerar med histidin imidazolringens Nδ, deprotonerade amidkväven hos de därpå följande glycinerna samt karbonylsyret hos den andra glycinen. Simuleringarna kunde visa att kopparjonen inte stabilt binder några axiella vattenmolekyler i lösning, till skillnad från en kristallstruktur av koordinationsstrukturen. Indolringen hos tryptofan interagerar direkt med kopparjonen genom stabiliserande katjon-π växelverkan utan direkt medverkan av någon vattenmolekyl. Växelverkan mellan indolringen och kopparjonen var väldefinierad och observerades kunna ske på båda sidor av koordinationsplanet. Molekyldynamiksimuleringarna med kopparjoner och oktapeptidområdet visade hur närvaron av kopparjoner ledde till ett mer strukturerat oktapeptidområde. / The copper-binding ability of the prion protein is thought to be closely related to its function. The human prion protein contains a copper-binding octapeptide region, where the octapeptide PHGGGWGQ is repeated four times consecutively. This work focuses on investigation of the structure and the dynamics of the octapeptide region by means of theoretical methods. Quantum chemical structural optimization allowed a detailed comparison of the interaction of several cations at the copper coordination site. These calculations identified rhodium(III) as a potent substitute for copper(II) that could be used to study the coordination site with NMR-spectroscopic methods. Solvation models that could be used in molecular dynamics simulations as an alternative to periodic boundary conditions were evaluated. Periodic boundary conditions are the best method for modeling the aqueous bulk in the kind of systems that are studied in this work. Molecular dynamics simulations were used to compare the behavior of the octapeptide region in the absence and presence of copper ions. Interaction between nonpolar rings strongly influences the structure of the region in the absence of copper ions. Four different non-bonded and bonded models for describing the interaction between copper and the protein were evaluated. Theoretical EXAFS spectra were calculated from the simulated structures. The results obtained for the bonded model are nearly identical with experimental data, which validates the use of the bonded model. This work thus shows strong evidence for copper(II) ions interacting with the octapeptide region through the histidine imidazole Nδ, the deprotonated nitrogen atoms of the following two glycine residues and the carbonyl oxygen atom of the second glycine residue. Notably, the simulations show that the axial sites of the copper ion do not stably coordinate water molecules in solution, as opposed to the crystal structure reported for the coordination site. Instead, the tryptophan indole ring interacted directly with the copper ion through stabilizing cation-π interaction without water mediation. The interaction of the indole ring with the copper ion was well-defined and was observed to occur on both sides of the coordination plane. The investigations of the interaction between copper ions and the octapeptide region with molecular dynamics simulations show how the presence of copper ions results in a more structured octapeptide region. / QC 20100816

This thesis deals with quantum chemistry methods for large systems. In particular, the thesis focuses on the efficient construction of the Coulomb and exchange matrices which are important parts of the Fock matrix in Hartree-Fock calculations. Density matrix purification, which is a method used to construct the density matrix for a given Fock matrix, is also discussed. The methods described are not only applicable in the Hartree-Fock case, but also in Kohn-Sham Density Functional Theory calculations, where the Coulomb and exchange matrices are parts of the Kohn-Sham matrix. Screening techniques for reducing the computational complexity of both Coulomb and exchange computations are discussed, including the fast multipole method, used for efficient computation of the Coulomb matrix. The thesis also discusses how sparsity in the matrices occurring in Hartree-Fock and Kohn-Sham Density Functional Theory calculations can be used to achieve more efficient storage of matrices as well as more efficient operations on them. / QC 20100817

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. / QC 20100820

The main theme of this thesis is to study effects of different environments on geometric and electronic structures, as well as optical responses, of molecules using time-(in)dependent density functional theory. Theoretical calculations have been carried out for properties that can be measured by conventional and advanced experimental techniques, including one-photon absorption (OPA), two-photon absorption (TPA), surface-enhanced Raman scattering (SERS) and second order nonlinear optical (NLO) response. The obtained good agreement between the theory and the experiment allows to further extract useful information about inter- and intra-molecular interactions that are not accessible experimentally. By comparing calculated one-photon absorption spectra of aluminum phthalocyanine chloride (AlPcCl) and AlPcCl -water complexes with the corresponding experiments, detailed information about the interaction between water molecules and AlPcCl, and geometric changes of AlPcCl molecule has been obtained. Effects of aggregation on two-photon absorption spectra of octupolar molecules have been examined. It is shown that the formation of clusters through inter-molecular hydrogen bonding can drastically change profiles of TPA spectra. It has also demonstrated that a well designed molecular aggregate/cluster, dendrimer, can enhance the second order nonlinear optical response of the molecules. In collaboration with experimentalists, a series of end-capped triply branched dendritic chromophores have been characterized, which can lead to large enhancement of the second order NLO property when the dipoles of the three branches in the dendrimers are highly parallelized. Surface-enhanced Raman scattering has made the detection of single molecules on metal surface become possible. Chemically bonded molecule-metal systems have been extensively studied. We have shown in a joint experimental and theoretical work that stable Raman spectra of a non-bonding molecule, perylene, physically adsorbed on Ag nano-particles can also be observed at low temperature. It is found that the local enhanced field has a tendency to drive molecule toward a gap of two closely lying nano-particles. The trapped molecule can thus provide a stable Raman spectrum with high resolution when its thermal motion is reduced at low temperature. For the ever growing size of molecular complexes, there is always the need to develop new computational methods. A conceptually simple but computationally efficient method, named as central insertion scheme (CIS), is proposed that allows to calculate electronic structure of quasi-periodic system containing more than 100,000 electrons at density functional theory levels. It enables to monitor the evolution of electronic structure with respect to the size of the system. / QC 20100823

During attempted enzyme-catalysed resolution of sterically hindered secondary alcohols, hemiacetals and their esters were unexpectedly detected. Hemiacetal esters are reactive compounds that decompose to alcohol, aldehyde and acid under ordinary work-up conditions i.e. in contact with water, acid, or silica gel. Thus, the presence of these side products might decrease the enantiomeric excess of the residual alcohol after workup of a lipase-catalysed resolution. The formation of these hemiacetal esters were further studied using both terpenoid and non-terpenoid substrate alcohols, various acyl donors, and lipases. The prerequisite for their formation is the presence of a sterically hindered substrate alcohol, an aldehyde or an aldehyde releasing acyl donor, and a lipase (PCL-L6, PCL-PS and CAL-B). Enantioselective synthesis of (S)- and (R)-cryptone was performed via a ring closing metathesis (RCM) of (S)- and (R)-6-isopropyl-1,7-octadien-3-one. The stereochemistry was induced by using pseudoephedrine as chiral auxiliary in an alkylation reaction which provided a chiral octadienone. Problems with removal of the RCM-catalyst resulted in low yields and low enantiomeric purity. In an alternative approach, racemic cryptone was subjected to conjugate addition with thiophenol followed by reduction to the corresponding alcohol. Lipase-catalysed resolution of this alcohol yielded, after oxidation and elimination, (R)- and (S)- cryptone with 76% and 98% ee, respectively. Marine fouling of immersed objects is a serious problem. Many coatings contain effective antifouling compounds having the drawback of being toxic to the marine environment. The marine natural product 10-isocyano-4-cadinene is a potentially non-toxic antifouling agent against the barnacle Balanus amphitrite and therefore an interesting target for organic synthesis. Cryptone was used as a starting material in attempted syntheses of this compound and other similar model compounds. / QC 20100901

About 90% of all chemicals are produced with the help of catalysts, substances with the ability to accelerate reactions without being consumed. Metal oxides play a prominent role in catalysis, since they are able to act reversibly in many chemical processes. Zink oxide (ZnO) is used to catalyse a number of industrially important reactions. For many of these reactions water is present as a reactant, product, or byproduct. The surface structure has a significant impact on the catalytic activity. However, currently, no experimental method simultaneously offers the spatial and temporal resolution to directly follow a catalytic process. This thesis explores surface structure dependent dynamical behavior for ZnO surfaces, nanoparticles, and water interfaces, using the computational chemistry method Molecular Dynamics, which enables detailed studies of structural and dynamical processes. Quantum mechanical (QM) calculations have been performed to obtain the energetics of the materials as a function of structure. This data has been used to parametrize reactive force-fields (ReaxFF), since the catalytic processes require both far larger and longer simulations than the capabilities of QM calculations on current computers. The simulations show that when steps are present on the surface, during crystal growth of ZnO, the creation of energetically favorable structures is accelerated. At the ZnO - water interface, structures that favor hydrogen bonding is promoted. At low, monolayer, coverage water adsorbs both molecularly and dissociatively, whereas at high coverage dissociated adsorption is favored. During evaporation from the monolayers, the ratio of dissociated and molecular water is preserved. Surface steps stabilizes the dissociated state as well as increases the rate of dissociation. The dynamical properties of ZnO nanoparticles were explored using Raman measurements and simulation. In both simulation and experiment certain vibrations were suppressed in the nanoparticles, compared to bulk. The simulations show that a narrow surface region lack the bulk-specific vibrations.

The number of poorly water-soluble drug substances in the pharmaceutical pipeline is increasing, and thereby also the need to design effective drug delivery systems providing high bioavailability. One favourable formulation approach is preparation of solid dispersions, where dispersing a poorly water-soluble drug in a water-soluble polymer matrix improves the dissolution behaviour and the bioavailability of the drug. However, in order to take full advantage of such formulations the impact of material properties on their performance needs to be investigated.   An experimental toolbox has been designed, and applied, for analysing the processes which govern the behaviour of solid pharmaceutical formulations in general, and that of solid dispersions in particular. For the purpose of monitoring multifaceted phenomena in situ during tablet dissolution, nuclear magnetic resonance (NMR) spectroscopy and NMR imaging are superior to many other techniques, both on macroscopic and molecular levels. The versatility of NMR with its isotope and chemical selectivity allows one to follow the influence of the original tablet properties on polymer mobilisation, drug migration and water penetration selectively. Mapping these processes on relevant time scales in dissolving tablets highlighted the gel layer inhomogeneity below the originally dry tablet surface as a key factor for drug release kinetics.   Furthermore, NMR relaxometry has been shown to provide novel information about the particle size of the drug and its recrystallisation behaviour within swelling solid dispersions. The NMR experiments have been complemented and supported by investigation of the crystalline state, the powder morphology and the surface composition of the dry solid dispersions. These experiments have been performed by X-ray photoelectron spectroscopy (XPS),  scanning electron microscopy (SEM), powder X-ray diffraction (pXRD), differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR) and dynamic contact angle (DAT) measurements.   The methods presented in this thesis provide a new avenue towards better understanding of the behaviour of solid dispersions, which in turn may result in more effective distribution of promising drug candidates despite their low water-solubility. / En allt större andel av de läkemedelssubstanser som idag är av intresse för den farmaceutiska industrin är svårlösliga i vatten. För att trots detta erhålla hög biotillgänglighet måste man utveckla beredningsformer som medger effektiv frisättning av den aktiva substansen. En lovande sådan beredningsform utgörs av fasta dispersioner, där den svårlösliga substansen finfördelas i en vattenlöslig polymer. För att utnyttja dessa dispersioners potential fullt ut måste dock materialegenskapernas inverkan på deras beteende kartläggas i större utsträckning än vad som tidigare gjorts.   En uppsättning experimentella metoder har i detta arbete utvecklats och använts för att analysera de processer som styr beteendet hos fasta läkemedelsberedningar i allmänhet, och fasta dispersioner i synnerhet. För observation av sådana processer in situ, under pågående tablettupplösning, är NMR-spektroskopi (kärnmagnetisk resonans-spektroskopi) och NMR-avbildning överlägsna många andra tekniker, både på makroskopisk och på molekylär nivå. NMR är en mångsidig metod med både isotop- och kemisk selektivitet. Genom att utnyttja dessa möjligheter kan de enskilda sambanden mellan den ursprungliga tablettens materialegenskaper och polymermobilisering, vatteninträngning och den aktiva substansens migrering följas separat. Kartläggning av dessa processer, på relevanta tidsskalor i tabletter under upplösning, påvisar att gellagrets inhomogenitet inuti den ursprungliga tabletten har stor betydelse för frisättningskinetiken.   Vidare visar sig NMR-relaxometri ge värdefull information om den aktiva substansens partikelstorlek och dess omkristallisationsbeteende i fasta dispersioner under svällning och upplösning. NMR-experimenten kompletteras med oberoende karakterisering av det kristallina tillståndet, pulvermorfologin och ytsammansättningen hos de torra fasta dispersionerna. Dessa experiment utförs med hjälp av XPS (röntgen-fotoelektronspektroskopi), SEM (elektronmikroskopi), pXRD (pulver-röntgendiffraktion), DCS (differentiell kalorimetri), FTIR (infraröd Fourier transform spektroskopi) och DAT (dynamisk kontaktvinkel) mätningar.   De metoder som presenteras i den här avhandlingen pekar mot nya vägar att nå djupare förståelse för beteendet hos fasta dispersioner, vilket i sin tur kan leda till att fler lovande läkemedelssubstanser kan distribueras effektivt trots begränsad vattenlöslighet. / QC 20100915