Här undersöks en strategi som behandlar dendrittillväxt på en solid litiumanod i ett litiumbatteri. Med hjälp av täthetfunktionalsteori adsorberades fyra flytande kristaller på litiumytan vilket ledde till en gränsskiktsstabilisering. Denna stabilisering har i en tidigare rapport länkats till dendrittillväxt i en fasfältsmodell. Fasfältsmodellen replikerades ej i denna rapport utan det ses som ett eventuellt nästa steg. Molekylerna interagerade starkt med ytan och de beräknade adsorptionsenergierna hade stor inverkan på litiumytans gränsskiktsenergi. De flytande kristallernas fas simulerades också, vilken hade en beräknad kohesivenergi i samma storleksordning som flytande vatten. Denna energi var lägre än adsorptionsenergierna, vilket tyder på att det finns en drivkraft för molekylerna att interagera med ytan. Vidare så undersöktes redoxstabiliteten hos molekylerna, där det visade sig att två av molekylerna hade LUMO-energier under Ferminivån hos litium. Dessa molekyler är således inte stabila nära litiumytan, utan kommer eventuellt ta del i elektrokemiska reaktioner. Slutligen så undersöktes diffusionsbarriären hos adsorberade litiumatomer. Här jämfördes barriären mellan fall då molekyler var adsorberade och inte, och det visade sig att med adsorberade molekyler så är diffusionsbarriären högre. / A strategy to suppress the growth of dendrites on solid state lithium anodes was investigated. Using density functional theory, four liquid crystal molecules were adsorbed on a solid lithium surface leading to an interfacial stabilization. This stabilization has earlier been used as a descriptor in a phase-field model which investigated dendrite suppression. The replication of this phase-field model was out of the scope of this thesis and left as future work. The LC molecules interacted strongly with the surface, and the calculated adsorption energies had an considerable impact on the interfacial energies of the lithium surface. A liquid crystal phase was also simulated, with a cohesive energy of the same magnitude as liquid water. This energy was lower than the adsorption energies, indicating that there is a driving force for the LC molcules to adsorb to the surface. Furthermore, the redox stability of the molecules in the proximity of the lithium surface was investigated, where two of them had LUMO energies below the Fermi level of lithium. Those two molecules were thus not considered sufficiently stable to not take part in any electrochemical reactions with solid lithium. Finally, the surface diffusion barrier of adsorbed lithium atoms was investigated. The barrier with and without the liquid crystals adsorbed to the surface was compared, which showed that the diffusion barrier was even higher with the molecules adsorbed.

No description available.

The aim of this study is to study the ground-state of various elements including Hydrogen molecules and Heliumatoms using a self written Density Functional Theory code. We limit ourselves to simple linear moleculesusing cylindrical symmetry, for which the computational difficulty is manageable and appropriate for anundergraduate thesis. We focus on the binding length and energy of the molecules stated here. Charge densityis calculated using the Poisson equation, which is used to calculate the potential and correlation potential. From the distance dependent of the total energy, the chemical bond length can be determined. The results showa total energy for a Hydrogen molecule is -31.3 eV and most optimal binding length is identified at 0.76 Å.

A theoretical framework for calculating electron transport through molecular junctions is presented. It is based on scattering theory using a Green's function formalism. The model can take both elastic and inelastic scattering into account and treats chemical and physical bonds on equal footing. It is shown that it is quite reliable with respect to the choice of functional and basis set. Applications concerning both elastic and inelastic transport are presented, though the emphasis is on the inelastic transport properties. The elastic scattering application part is divided in two part. The first part demonstrates how the current magnitude is strongly related to the junction width, which provides an explanation why experimentalists get two orders of magnitude differences when performing measurements on the same type of system. The second part is devoted to a study of how hydrogenbonding affects the current-voltage (I-V) characteristics. It is shown that for a conjugated molecule with functional groups, the effects can be quite dramatic. This shows the importance of taking possible intermolecular interactions into account when evaluating and comparing experimental data. The inelastic scattering part is devoted to get accurate predictions of inelastic electron tunneling spectroscopy (IETS) experiments. The emphasis has been on elucidating the importance of various bonding conditions for the IETS. It is shown that the IETS is very sensitive to the shape of the electrodes and it can also be used to discriminate between different intramolecular conformations. Temperature dependence is nicely reproduced. The junction width is shown to be of importance and comparisons between experiment as well as other theoretical predictions are made. / QC 20101118

The Empirical Valence Bond (EVB) method has long been recognised as a reliable approach for the calculation of free energies of reactions in heterogeneous electrochemical environments. In spite of its established efficacy, existing implementations and protocols often pose challenges due to their tediousness or lack of transparency. This work introduces an open-source Python implementation of the EVB method, specifically designed to enhance accessibility and comprehension of the method making it highly suited for educational purposes. Recommendations are provided for integrating the methodology into the GROMACS application programming interface, to facilitate its integration into computational chemistry workflows and accellerating research. The program is demonstrated through various computations, including a short EVB study on the dissociation of \COt and tetraphenylporphyrin in the vicinity of a graphene sheet in water and dimethylformamide. Moreover, a novel analytical expression for computing the free energy profile is presented, showing promising agreement with the canonical discretised method.

No description available.

Enolate formation by proton abstraction from an sp3-hybridized carbon atom situated next to a carbonyl or carboxylate group is an abundant process in nature. Since the corresponding nonenzymatic process in water is slow and unfavorable due to high intrinsic free energy barriers and high substrate pKa s, enzymes catalyzing such reaction steps must overcome both kinetic and thermodynamic obstacles. Computer simulations were used to study enolate formation catalyzed by glyoxalase I (GlxI) and 3-oxo-Δ5-steroid isomerase (KSI). The results, which reproduce experimental kinetic data, indicate that for both enzymes the free energy barrier reduction originates mainly from the balancing of substrate and catalytic base pKas. This was found to be accomplished primarily by electrostatic interactions. The results also suggest that the remaining barrier reduction can be explained by the lower reorganization energy in the preorganized enzyme compared to the solution reaction. Moreover, it seems that quantum effects, arising from zero-point vibrations and proton tunnelling, do not contribute significantly to the barrier reduction in GlxI. For KSI, the formation of a low-barrier hydrogen bond between the enzyme and the enolate, which is suggested to stabilize the enolate, was investigated and found unlikely. The low pKa of the catalytic base in the nonpolar active site of KSI may possibly be explained by the presence of a water molecule not detected by experiments. The hemoglobin-degrading aspartic proteases plasmepsinI and plasmepsin II from Plasmodium falciparum have emerged as putative drug targets against malaria. A series of C2- symmetric compounds with a 1,2-dihydroxyethylene scaffold were investigated for plasmepsin affinity, using computer simulations and enzyme inhibition assays. The calculations correctly predicted the stereochemical preferences of the scaffold and the effect of chemical modifications. Calculated absolute binding free energies reproduced experimental data well. As these inhibitors have down to subnanomolar inhibition constants of the plasmepsins and no measurable affinity to human cathepsin D, they constitute promising lead compounds for further drug development.

5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.

The reaction mechanisms for the hemoglobin degrading enzymes in the Plasmodium falciparum malaria parasite, plasmepsin II (Plm II) and histo-aspartic protease (HAP), have been analyzed by molecular simulations. The reaction free energy profiles, calculated by the empirical valence bond (EVB) method in combination with molecular dynamics (MD) and free energy perturbation (FEP) simulations are in good agreement with experimental data. Additional computational methods, such as homology modelling and automated substrate docking, were necessary to generate a 3D model and a reactive substrate conformation before the reaction mechanism in HAP could be investigated. HAP is found to be an aspartic protease with a peptide cleaving mechanism similar to plasmepsin II. The major difference between these enzymes is that the negatively charged tetrahedral intermediate is stabilized by the charged histidine in HAP while in Plm II it is a neutral aspartic acid. Also the reaction mechanism for two other aspartic proteases, cathepsin D and HIV-1 protease, was simulated. These enzymes are relevant both for the inhibitor selectivity and for obtaining a general picture of catalysis in aspartic proteases. Another project involves inhibitor design towards plasmepsins. In particular, Plm II directed inhibitors based on the dihydroxyethylene scaffold have been characterized computationally. Molecular dynamics (MD) simulations were used to propagate the investigated system through time and to generate ensembles used for the calculation of free energies. The ligand binding affinities were calculated with the linear interaction energy (LIE) method. The most potent inhibitor had a Ki value of 6 nM and showed 78 % parasite inhibition when tested on red blood cells infected by malaria parasite P. falciparum. Citrate synthase is part of the citric acid cycle and is present in organisms that live in cold sea water as well as hot springs. The temperature adaptation of citrate synthase to cold and heat was investigated in terms of the difference in transition state stabilization between the psychrophilic, mesophilic and hyperthermophilic homologues. The EVB, FEP and MD methods were used to generate reaction free energy profiles. The investigated energetics points toward the electrostatic stabilization during the reaction as the major difference between the different citrate synthase homologues. The electrostatic stabilization of the transition state is most effective in the following order of the citrate synthase homologues: hyperthermophile, mesophile, psycrophile. This could be a general rule for temperature adaptation of enzyme catalysis.

Knowledge about the insertion and stabilization of membrane proteins is a key step towards understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic to insert efficiently, but there are many exceptions with unfavorable polar or titratable residues. Since evolutionary conserved these amino acids are likely of paramount functional importance, e.g. the four arginines in the S4 voltage sensor helix of voltage-gated ion channels. This has lead to vivid discussion about their conformation, protonation state and cost of insertion. To address such questions, the main focus of this thesis has been membrane protein solvation in lipid bilayers, evaluated using molecular dynamics simulations methods. A main result is that polar and charged amino acids tend to deform the bilayer by pulling water/head-groups into the hydrophobic core to keep their hydrogen bonds paired, thus demonstrating the adaptiveness of the membrane to allow specific and quite complex solvation. In addition, this retained hydration suggests that the solvation cost is mainly due to entropy, not enthalpy loss. To further quantify solvation properties, free energy profiles were calculated for all amino acids in pure bilayers, with shapes correlating well with experimental in vivo values but with higher magnitudes. Additional profiles were calculated for different protonation states of the titratable amino acids, varying lipid composition and with transmembrane helices present in the bilayer. While the two first both influence solvation properties, the latter seems to be a critical aspect. When the protein fraction in the models resemble biological membranes, the solvation cost drops significantly - even to values compatible with experiment. In conclusion, by using simulation based methods I have been able to provide atomic scale explanations to experimental results, and in particular present a hypothesis for how the solvation of charged groups occurs.