<p>Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: <i>zinc-containing peptidases</i> (thermolysin and stromelysin),<i> methyl-coenzyme M reductase</i>, <i>ribonucleotide reductases</i> (classes I and III), and <i>superoxide dismutases</i> (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.</p>

<p>The serendipitous discovery of the potent cytotoxic properties of cisplatin brought about a revolution in the treatment of certain types of cancer, but almost fifty years later, there still remain unknown areas in the chemistry of cisplatin. There are questions regarding which form of the drug reaches its DNA target, or why certain DNA sequences are more preferred than others for reaction with cisplatin. The work presented here aims to address some of these problems, using quantum chemical calculations to complement and interpret available experimental data.</p><p>Cisplatin's activation reactions are explored by Density Functional Theory (DFT) on two model systems, one solely using a self-consistent reaction field (SCRF) for modeling bulk water, and one including an additional partial solvation shell of water molecules. It is concluded that adding explicit solvation provides a better picture than using SCRF solvation alone. The energy surface supports the view that the active form of cisplatin is the monoaquated form.</p><p>The activation reactions of the cisplatin-derived drug, JM118, are investigated using DFT and SCRF calculations using three solvation model systems. The results show a slower rate of hydrolysis for the first reaction, and a faster rate for the second, suggesting diaquated JM118 as the main DNA binding form of the drug.</p><p>Diaquated cisplatin's first and second reaction with guanine and adenine are studied using DFT and SCRF solvation. Cisplatin's propensity toward guanine in the first substitution is explained by larger stabilisation energy for the initially formed complex and by favoured kinetics. For the second substitution, higher stability in complexation with guanine over adenine is ascribed as the main factor favouring guanine over adenine substitution. This provides the first explanation for the predominance of 1,2-d(GpG) over 1,2-d(ApG) adducts, and the direction specificity of the 1,2-d(ApG) adducts.</p>

Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: zinc-containing peptidases (thermolysin and stromelysin), methyl-coenzyme M reductase, ribonucleotide reductases (classes I and III), and superoxide dismutases (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.

The serendipitous discovery of the potent cytotoxic properties of cisplatin brought about a revolution in the treatment of certain types of cancer, but almost fifty years later, there still remain unknown areas in the chemistry of cisplatin. There are questions regarding which form of the drug reaches its DNA target, or why certain DNA sequences are more preferred than others for reaction with cisplatin. The work presented here aims to address some of these problems, using quantum chemical calculations to complement and interpret available experimental data. Cisplatin's activation reactions are explored by Density Functional Theory (DFT) on two model systems, one solely using a self-consistent reaction field (SCRF) for modeling bulk water, and one including an additional partial solvation shell of water molecules. It is concluded that adding explicit solvation provides a better picture than using SCRF solvation alone. The energy surface supports the view that the active form of cisplatin is the monoaquated form. The activation reactions of the cisplatin-derived drug, JM118, are investigated using DFT and SCRF calculations using three solvation model systems. The results show a slower rate of hydrolysis for the first reaction, and a faster rate for the second, suggesting diaquated JM118 as the main DNA binding form of the drug. Diaquated cisplatin's first and second reaction with guanine and adenine are studied using DFT and SCRF solvation. Cisplatin's propensity toward guanine in the first substitution is explained by larger stabilisation energy for the initially formed complex and by favoured kinetics. For the second substitution, higher stability in complexation with guanine over adenine is ascribed as the main factor favouring guanine over adenine substitution. This provides the first explanation for the predominance of 1,2-d(GpG) over 1,2-d(ApG) adducts, and the direction specificity of the 1,2-d(ApG) adducts.

The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed.   In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods.   For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers.   For the two tungstoenzymes, several different mechanistic scenarios have been considered to identify the energetically most feasible one. For both enzymes, new mechanisms are proposed.   Finally, the mechanism of mycolic acid cyclopropane synthase has been shown to be a direct methyl transfer to the substrate double bond, followed by proton transfer to the bicarbonate.   From the studies of these enzymes, we demonstrate that density functional calculations are able to solve mechanistic problems related to enzymatic reactions, and a wealth of new insight can be obtained.

To enable future environmentally friendly access to space by means of solid rocket propulsion a viable replacement to the hazardous ammonium perchlorate oxidizer is needed. Ammonium dinitramide (ADN) is one of few such compounds currently known. Unfortunately compatibility issues with many polymer binder systems and unexplained solid-state behavior have thus far hampered the development of ADN-based propellants. Chapters one, two and three offer a general introduction to the thesis, and into relevant aspects of quantum chemistry and polymer chemistry. Chapter four of this thesis presents extensive quantum chemical and spectroscopic studies that explain much of ADN’s anomalous reactivity, solid-state behavior and thermal stability. Polarization of surface dinitramide anions has been identified as the main reason for the decreased stability of solid ADN, and theoretical models have been developed to explain and predict the solid-state stability of general dinitramide salts. Experimental decomposition characteristics for ADN, such as activation energy and decomposition products, have been explained for different physical conditions. The reactivity of ADN towards many chemical groups is explained by ammonium-mediated conjugate addition reactions. It is predicted that ADN can be stabilized by changing the surface chemistry with additives, for example by using hydrogen bond donors, and by trapping radical intermediates using suitable amine-functionalities. Chapter five presents several conceptual green energetic materials (GEMs), including different pentazolate derivatives, which have been subjected to thorough theoretical studies. One of these, trinitramide (TNA), has been synthesized and characterized by vibrational and nuclear magnetic resonance spectroscopy. Finally, chapter six covers the synthesis of several polymeric materials based on polyoxetanes, which have been tested for compatibility with ADN. Successful formation of polymer matrices based on the ADN-compatible polyglycidyl azide polymer (GAP) has been demonstrated using a novel type of macromolecular curing agent. In light of these results further work towards ADN-propellants is strongly encouraged. / QC 20101103

This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions. K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell reproduced by linear combinations of composed base pairs weighted by their ratio. The NEXAFS spectra study has been extended to other realistic systems. We have used cluster modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics. Multi-scale computational study on four short peptides in a self-assembled cage is presented. It isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage. Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules. / QC 20110404

Multivariate regression of several different quantum chemical descriptors was used to build a model for the reactivity of nucleophilic aromatic substitution reactions, i.e. SNAr reactions, through predictingthe molecular reaction site’s Gibb’s free activation energy (ΔG‡). The datasets used for training provided data of ΔG‡ for several differing halide leaving groups including chloride, bromide, and fluoride. A set of descriptors were tested for the different leaving groups revealing that dissimilar leaving groups are more dependent on certain descriptors than others, meaning each model has to be tailored for the specific leaving groups. Excellent correlations (R2 = 0.93) were achieved between the predicted ΔG‡ and the experimental ΔG‡.The ability of the model to predict regioselectivity in aromatic compounds with multiple leaving groups was tested and successfully predicted the correct regioselectivity through the calculation of ΔΔG‡ in each case tested. However, the model’s validity outside of the training dataset was put into doubt through low R2 values when the model was tested with several external datasets. An unknown factor arose which is speculated to be because of how differing nucleophiles and solvents affect the ΔG‡. One of these tests yielded excellent correlations (R2 = 0.9525) which could be because of similarities between solvents and nucleophiles between the training dataset but a similar factor between predicted ΔG‡ and the experimental ΔG‡ could still be observed.

In this thesis, a method to calculate eigenpairs is implemented for the Multipsi library. While the standard implemtentations use the Davidson method with Rayleigh-Ritz extraction to calculate the eigenpairs with the lowest eigenvalues, the new method uses the harmonic Davidson method with the harmonic Rayleigh-Ritz extraction to calculate eigenpairs with eigenvalues near a chosen target. This is done for Configuration Interaction calculations and for Multiconfigurational methods. From calculations, it seems the new addition to the Multipsi library is worth investigating further as convergence for difficult systems with a lot of near-degeneracy was improved. / I denna avhandling implementeras en metod för att beräkna egenpar för Multipsi-biblioteket. Medan standardimplementeringarna använder Davidson-metoden med Rayleigh-Ritz-extraktion för att beräkna egenparen med de lägsta egenvärdena, använder den nya metoden den harmoniska Davidson-metoden med den harmoniska Rayleigh-Ritz-extraktionen för att beräkna egenparen med egenvärden nära ett valt mål. Detta görs för konfigurationsinteraktionsberäkningar och för multikonfigurationsmetoder. Utifrån beräkningarna verkar det nya tillskottet till Multipsi-biblioteket vara värt att undersöka vidare eftersom konvergensen för svåra system med mycket nära degenerering förbättrades.

<p>Quantum chemical calculations have been performed to investigate radical cation rearrangement, radical carbonylation, and homolytic substitution reactions of organic molecules.</p><p>The rearrangement of the bicyclopropylidiene radical cation to the tetramethyleneethane radical cation is predicted to proceed with stepwise disrotatory opening of the two rings. Each ring opening is found to be combined with a striking pyramidalization of a carbon atom in the central bond.</p><p>The isomerization of the norbornadiene radical cation to the cycloheptatriene radical cation (<b>CHT</b><b>.+</b>), initialized by opening of a bridgehead–methylene bond, is investigated. The most favorable path involves concerted rearrangement to the norcaradiene radical cation followed by ring opening to <b>CHT</b><b>.+</b>. The barrier of this channel is found to be significantly reduced upon substitution of the methylene group with C(CH₃)₂.</p><p>Stepwise mechanisms are predicted to be favored over concerted isomerization for the McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal. The barrier for the concerted rearrangement is found to be lowered by 17.2 kcal/mol upon substitution, a result which is rationalized by the calculated dipole moments and atomic charges.</p><p>Recent experiments showed that photoinitiated carbonylation of alkyl iodides with [¹¹C]carbon monoxide may be significantly enhanced by using small amounts of ketones that have nπ* character of their excited triplet state. DFT calculations show the feasibility of an atom transfer type mechanism, proposed to explain these observations. Moreover, the computational results rationalize the observed differences in yield when using various alcohol solvents.</p><p>Finally, following photolysis of methyliodide, recent electron spin resonance spectroscopy experiments demonstrated that the S_H2 reaction ^•CD₃ + SiD₃CH₃ → CD₃SiD₃ + ^•CH₃ proceeds with high selectivity over the energetically more favorable D abstraction. The role of geometrical effects, especially the formation of prereactive complexes between methylsilane and methyliodide is studied, and a plausible explanation for the experimentally observed paradox is presented.</p>