Dissertations / Theses on the topic 'Quantum Chemical Computation'
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Green, Anthony James. "Computation of hydrogen bond basicity as a descriptor in bioisosterism : a quantum chemical topology perspective." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/computation-of-hydrogen-bond-basicity-as-a-descriptor-in-bioisosterism-a-quantum-chemical-topology-perspective(068da139-48b0-4881-a131-5c281fd4af8a).html.
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Hydrogen bonding is a regularly occurring non covalent interaction in biological systems. Hydrogen bonding can influence a drug’s interaction with its target. It is therefore important to practically measure the relative strengths of hydrogen bonds. Hydrogen bond basicity is a measure of a hydrogen bond acceptor’s capacity to accept hydrogen bonds. There are many hydrogen bond basicity scales. However, the pKBHX scale is claimed to be the most relevant to medicinal chemists because it gives a thermodynamically deducible values for each site in polyfunctional bases. A computed property, the change in energy of the hydrogen bond donor hydrogen bond atom ΔE(H), derived from the quantum theory of atoms in molecules has been found to correlate strongly with pKBHX values for OH and NH hydrogen bond donors. In particular, R2 values of 0.95 and 0.97 have been found when methanol and methylamine respectively are used as hydrogen bond donors. The property ΔE(H) has also been successfully used to predict the pKBHX values of an external data set and the values of polyfunctional bases. The strength of the correlations are not dramatically affected by using scaled down fragments of bases, or by relaxing the convergence criteria during the geometry optimisation step of calculations. The relationship between ΔE(H) and pKBHX has been found to break down for tertiary amines, and more generally for strong proton acceptors with pKBH+ values greater than 6. The successful pKBHX prediction model was, however, unsuccessful in predicting drug binding data and pKBHX values of bases that accept two separate hydrogen bonds. At this moment in time both the reason why the relationship between pKBHX and ΔE(H) is present and then breaks down for strong proton acceptors is unfortunately unknown.
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Faglioni, Francesco Goddard William A. "Quantum chemical computations of heterogeneous selective oxidation, STM images, and multiple bond reactions." Diss., Pasadena, Calif. : California Institute of Technology, 1998. http://resolver.caltech.edu/CaltechTHESIS:10202009-092753223.
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Remmert, Sarah M. "Reduced dimensionality quantum dynamics of chemical reactions." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:7f96405f-105c-4ca3-9b8a-06f77d84606a.
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In this thesis a reduced dimensionality quantum scattering model is applied to the study of polyatomic reactions of type X + CH4 <--> XH + CH3. Two dimensional quantum scattering of the symmetric hydrogen exchange reaction CH3+CH4 <--> CH4+CH3 is performed on an 18-parameter double-Morse analytical function derived from ab initio calculations at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. Spectator mode motion is approximately treated via inclusion of curvilinear or rectilinear projected zero-point energies in the potential surface. The close-coupled equations are solved using R-matrix propagation. The state-to-state probabilities and integral and differential cross sections show the reaction to be primarily vibrationally adiabatic and backwards scattered. Quantum properties such as heavy-light-heavy oscillating reactivity and resonance features significantly influence the reaction dynamics. Deuterium substitution at the primary site is the dominant kinetic isotope effect. Thermal rate constants are in excellent agreement with experiment. The method is also applied to the study of electronically nonadiabatic transitions in the CH3 + HCl <--> CH4 + Cl(2PJ) reaction. Electrovibrational basis sets are used to construct the close-coupled equations, which are solved via Rmatrix propagation using a system of three potential energy surfaces coupled by spin-orbit interaction. Ground and excited electronic surfaces are developed using a 29-parameter double-Morse function with ab initio data at the CCSD(T)/ccpV( Q+d)Z-dk//MP2/cc-pV(T+d)Z-dk level of theory, and with basis set extrapolated data, both corrected via curvilinear projected spectator zero-point energies. Coupling surfaces are developed by fitting MCSCF/cc-pV(T+d)Z-dk ab initio spin orbit constants to 8-parameter functions. Scattering calculations are performed for the ground adiabatic and coupled surface models, and reaction probabilities, thermal rate constants and integral and differential cross sections are presented. Thermal rate constants on the basis set extrapolated surface are in excellent agreement with experiment. Characterisation of electronically nonadiabatic nonreactive and reactive transitions indicate the close correlation between vibrational excitation and nonadiabatic transition. A model for comparing the nonadiabatic cross section branching ratio to experiment is discussed.
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Fransson, Thomas. "Chemical bond analysis in the ten-electron series." Thesis, Linköping University, Department of Physics, Chemistry and Biology, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-19554.
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This thesis presents briefly the application of quantum mechanics on systems ofchemical interest, i.e., the field of quantum chemistry and computational chemistry.The molecules of the ten-electron series, hydrogen fluoride, water, ammonia,methane and neon, are taken as computational examples. Some applications ofquantum chemistry are then shown on these systems, with emphasis on the natureof the molecular bonds. Conceptual methods of chemistry and theoreticalchemistry for these systems are shown to be valid with some restrictions, as theseinterpretations does not represent physically measurable entities.The orbitals and orbital energies of neon is studied, the binding van der Waalsinteractionresulting in a Ne2 molecule is studied with a theoretical bond lengthof 3.23 °A and dissociation energy of 81.75 μEh. The equilibrium geometries ofFH, H2O, NH3 and CH4 are studied and the strength and character of the bondsinvolved evaluated using bond order, dipole moment, Mulliken population analysisand L¨owdin population analysis. The concept of electronegativity is studied in thecontext of electron transfer. Lastly, the barrier of inversion for NH3 is studied, withan obtained barrier height of 8.46 mEh and relatively constant electron transfer.
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Dağtepe, Pınar Elmacı Nuran. "A computational study on the structure of allene polymers by using quantum chemical methods/." [s.l.]: [s.n.], 2005. http://library.iyte.edu.tr/tezler/master/kimya/T000348.pdf.
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Phadungsukanan, Weerapong. "Building a computational chemistry database system for the kinetic studies in combustion." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648233.
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Rönnby, Karl. "Quantum Chemical Feasibility Study of Methylamines as Nitrogen Precursors in Chemical Vapor Deposition." Thesis, Linköpings universitet, Kemi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-132812.
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The possibility of using methylamines instead of ammonia as a nitrogen precursor for the CVD of nitrides is studied using quantum chemical computations of reaction energies: reaction electronic energy (Δ𝑟𝐸𝑒𝑙𝑒𝑐) reaction enthalpy (Δ𝑟𝐻) and reaction free energy (Δ𝑟𝐺). The reaction energies were calculated for three types of reactions: Uni- and bimolecular decomposition to more reactive nitrogen species, adduct forming with trimethylgallium (TMG) and trimethylaluminum (TMA) followed by a release of methane or ethane and surface adsorption to gallium nitride for both the unreacted ammonia or methylamines or the decomposition products. The calculations for the reaction entropy and free energy were made at both STP and CVD conditions (300°C-1300°C and 50 mbar). The ab inito Gaussian 4 (G4) theory were used for the calculations of the decomposition and adduct reactions while the surface adsorptions were calculated using the Density Functional Theory method B3LYP. From the reactions energies it can be concluded that the decomposition was facilitated by the increasing number of methyl groups on the nitrogen. The adducts with mono- and dimethylamine were more favorable than ammonia and trimethylamine. 𝑁𝐻2 was found to be most readily to adsorb to 𝐺𝑎𝑁 while the undecomposed ammonia and methylamines was not willingly to adsorb.
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Tekin, Emine Deniz. "Investigation Of Biologically Important Small Molecules: Quantum Chemical And Molecular Dynamics Calculations." Phd thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612343/index.pdf.
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In this thesis, six small molecules (S-allylcysteine, S-allyl mercaptocysteine, allicin, methyl propyl disulfide, allyl methyl sulfide and dipropylsulfide) that are found in garlic and onion, and are known to be beneficial for human health were studied using molecular mechanics, semi-empirical methods, ab-initio (Restricted Hartree Fock), and density functional theory. Using the same methods, a synthetic pyrethroid pesticide molecule, called cyfluthrin, was also studied. Structural, vibrational and electronic properties of these molecules were found. These theoretical studies could clarify the role of these molecules on human health before they are commercially developed and used. In addition, unfolding dynamics of small peptide sequences (DDATKTFT and its variants) in immunoglobulin G-binding protein G was investigated. Protein folding and unfolding is one of the most important unsolved problems in molecular biology. Because of the large number of atoms involved in protein folding, it is a massive computational problem. The hope is that, one could understand this mechanism with the help of molecular dynamics simulation on small peptides. One of our findings is that the location of the hydrogen bonds is important for the stability of the peptide.
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Parameswaran, Sreeja. "Solar Energy Conversion in Plants and Bacteria Studied Using FTIR Difference Spectroscopy and Quantum Chemical Computational Methodologies." Digital Archive @ GSU, 2009. http://digitalarchive.gsu.edu/phy_astr_diss/32.
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This dissertation presents a study of the molecular mechanism underlying the highly efficient solar energy conversion processes that occur in the Photosystem I (PS I) reaction centers in plants and bacteria. The primary electron donor P700 is at the heart of solar energy conversion process in PS I and the aim is to obtain a better understanding of the electronic and structural organization of P700 in the ground and excited states. Static Fourier Transform Infra-Red (FTIR) difference spectroscopy (DS) in combination with site directed mutagenesis and Density Functional Theory (DFT) based vibrational frequency simulations were used to investigate how protein interactions such as histidine ligation and hydrogen bonding modulate this organization. (P700+-P700) FTIR DS at 77K were obtained from a series of mutants from the cyanobacterium Synechocystis sp. 6803 (S. 6803) where the amino acid residues near the C=O groups of the two chlorophylls of P700 where specifically changed. (P700+-P700) FTIR DS was also obtained for a set of mutants from C. reinhardtii where the axial ligand to A0-, the primary electron acceptor in PS I was modified. The FTIR DS obtained from these mutants provides information on the axial ligands, the hydrogen bonding status as well as the polarity of the environment of specific functional groups that are part of the chlorophyll molecules that constitute P700. Assignment of the FTIR bands to vibrational modes in specific types of environment is very difficult. In order to assist the assignment of the difference bands in experimental spectra DFT based vibrational mode frequency calculations were undertaken for Chl-a and Chl-a+ model molecular systems under different set of conditions; in the gas phase, in solvents using the Polarizable Continuum Model (PCM), in the presence of explicit solvent molecules using QM/MM methods, and in the presence of axial ligands and hydrogen bonds. DFT methods were also used to calculate the charge, spin and redox properties of Chl-a/Chl-a’ dimer models that are representative of P700, the primary electron donor in PS I.
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Peterson, Charles Campbell. "Accurate Energetics Across the Periodic Table Via Quantum Chemistry." Thesis, University of North Texas, 2015. https://digital.library.unt.edu/ark:/67531/metadc822822/.
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Greater understanding and accurate predictions of structural, thermochemical, and spectroscopic properties of chemical compounds is critical for the advancements of not only basic science, but also in applications needed for the growth and health of the U.S. economy. This dissertation includes new ab initio composite approaches to predict accurate energetics of lanthanide-containing compounds including relativistic effects, and optimization of parameters for semi-empirical methods for transition metals. Studies of properties and energetics of chemical compounds through various computational methods are also the focus of this research, including the C-O bond cleavage of dimethyl ether by transition metal ions, the study of thermochemical and structural properties of small silicon containing compounds with the Multi-Reference correlation consistent Composite Approach, the development of a composite method for heavy element systems, spectroscopic of compounds containing noble gases and metals (ArxZn and ArxAg+ where x = 1, 2), and the effects due to Basis Set Superposition Error (BSSE) on these van der Waals complexes.
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Widdifield, Cory. "Multinuclear Solid-State Magnetic Resonance Studies on ‘Exotic’ Quadrupolar Nuclei: Acquisition Methods, High-Order Effects, Quantum Chemical Computations, and NMR Crystallography." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/20722.
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This dissertation attempts to extend the classes of halogen-containing systems which may be studied using solid-state nuclear magnetic resonance (SSNMR). As line shape broadening due to the quadrupolar interaction (QI) scales inversely with the applied field, high-field magnet technology is indispensable for this research. Combining advanced radiofrequency pulse sequences with high-field wideline data acquisition allowed for the collection of very broad SSNMR signals of all quadrupolar halogen nuclei (i.e., 35/37Cl, 79/81Br and 127I) within a reasonable amount of experimental time. The initial systems for study were of the MX2 variety (M = Mg, Ca, Sr, Ba; X = Cl, Br, I). In total, 9 anhydrous compounds were tested. The effects of hydrate formation were tested on 7 additional compounds. Systematic trends in the observed δiso values (and to a lesser extent, Ω and CQ) were found to be diagnostic of the extent of hydration in these materials. Resolving power was successfully tested using SrBr2, which possesses 4 magnetically unique sites. The composition of CaBr2•xH2O was convincingly determined using SSNMR data and the hydration trends noted above. The sensitivity of the QI to the local bonding environment (e.g., bond distance changes of less than 0.05 Å) was used to refine (when coupled with gauge-including projector augmented-wave density functional theory (GIPAW DFT) quantum chemical computations) the structure of MgBr2, and was used to correct prior NMR data for CaCl2 (earlier accounts had been performed upon a CaCl2 hydrate). During NMR data analysis of certain iodine-containing materials, it was found that standard fitting software (which uses perturbation theory) could not reproduce the observations. Proper analysis required the use of exact simulation software and allowed for the observation of high-order quadrupole-induced effects (HOQIE). This motivated further studies using rhenium-185/187 nuclei, where it was expected that HOQIE would be more dramatic. The observed rhenium SSNMR spectra possessed additional fine structure that had never been observed before experimentally, nor would be expected from currently-available perturbation theory analysis software. Lastly, preliminary results are shown where 127I SSNMR is used to study important supramolecular systems, and the composition of the popular synthetic reagent ‘GaI’ is elucidated.
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Crawford, Luke. "Mechanistic insights into enzymatic and homogeneous transition metal catalysis from quantum-chemical calculations." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/7818.
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Catalysis is a key area of chemistry. Through catalysis it is possible to achieve better synthetic routes, exploit molecules normally considered to be inactive and also attain novel chemical transformations. The development of new catalysts is crucial to furthering chemistry as a field. Computational chemistry, arising from applying the equations of quantum and classical mechanics to solving chemical problems, offers an essential route to investigating the underlying atomistic detail of catalysis. In this thesis calculations have been applied towards studying a number of different catalytic processes. The processing of renewable chemical sources via homogeneous reactions, specifically cardanol from cashew nuts, is discussed. All routes examined for monoreduction of a diene model by [Ru(H)(iPrOH)(Cl)(C₆H₆)] and [Ru(H)(iPrOH)(C₆H₆)]⁺ are energetically costly and would allow for total reduction of the diene if they were operating. While this accounts for the need of high temperatures, further work is required to elucidate the true mechanism of this small but surprisingly complex system. Gold-mediated protodecarboxylation was examined in tandem with experiment to find the subtle steric and electronic effects that dictate CO₂ extrusion from gold N-heterocyclic carbene activated benzene-derived carboxylic acids. The origin of a switch in the rate limiting step from decarboxylation to protodeauration with less activated substrates was also clearly demonstrated. Studies of gold systems are closed with examinations of 1,2-difluorobenzene C–H activation and CO₂ insertion by [Au(IPr)(OH)]. Calculations highlight that the proposed mechanism for oxazole-derived substrates cannot be extended to 1,2-difluorobenzene and instead a digold complex offers more congruent predicted kinetics. The lens of quantum chemistry was turned upon palladium-mediated methoxycarbonylation reactions. An extensive study was undertaken to attempt to understand the bidentate diphosphine ligand dependency on forming either methylpropanoate (MePro) or copolymers. Mechanisms currently suggested in literature are shown to be incongruous with the formation of MePro by Pd(OAc)₂ and bulky diphosphines. A possible alternative route is proposed in this thesis. Four mechanisms for methoxycarbonylation with Pd(2-PyPPh₂)ₙ are detailed. The most accessible route is found to be congruent with experimental reports of selectivity, acid dependency and slight steric modifications. A modification of 2-PyPPh₂ to 2-(4-NMe₂-6-Me)PyPPh₂ is shown to improve both selectivity and turnover, the latter by four orders of magnitude (highest transition state from 22.9 kcal/mol to 16.7 kcal/mol ∆G), and this new second generation in silico designed ligand is studied for its applicability to wider substrate scope and different solvents. The final chapter of this thesis is a mixed quantum mechanics and molecular mechanics (QM/MM) examination of an enzymatic reaction, discussing the need for certain conditions and the role of particular amino acid residues in an S[sub]N2 hydrolysis reaction.
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Singh, Neeraj, Benjamin Fiedler, Joachim Friedrich, and Klaus Banert. "Experimental observation and quantum chemical investigation of thallium(I) (Z)-methanediazotate: synthesis of a long sought and highly reactive species." Universitätsbibliothek Chemnitz, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-224226.
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For the first time, successful synthesis and characterisation of the missing (Z)-isomer of thallium(I) methanediazotate has been accomplished, utilising low-temperature NMR monitoring analysis. The title compound was synthesised from N-methyl-N-nitrosourea and thallium(I) propoxide, under sub-ambient temperature conditions, as a highly moisture sensitive entity. Quantum chemical calculations, performed at the CCSD(T) level, depict excellent conformity to experimental results. Indeed, compared to its (E) counterpart, the formation of the title compound is thermodynamically less favoured, but preferred by means of kinetic control owing to a hindered isomerisation.
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Hagelin, Alexander. "ZnO nanoparticles : synthesis of Ga-doped ZnO, oxygen gas sensing and quantum chemical investigation." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-64730.
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Doped ZnO nanoparticles were synthesized by three different methods – electrochemical deposition under oxidizing conditions (EDOC) , combustion method and wet chemical synthesis – for investigating the oxygen gas sensing response. Ga-doped ZnO was mostly synthesized but also In-doped ZnO was made. The samples were analyzed by XRD, SEM, EDX and TEM. Gas response curves are given alongside with Langmuir fitted curves and data for pure ZnO and Ga-doped ZnO. DFT quantum chemical investigation of cluster models ZnO nanoparticles were performed to evaluate defect effects and oxygen and nitrogen dioxide reactions with the ZnO surface. Defects were investigated by DOS and HOMO-LUMO plots , and are oxygen vacancy, zinc vacancy, zinc interstitial and gallium doping by replacing zinc with gallium. Oxygen and nitrogen dioxide reactions were investigated by computing Mulliken charges, bond lengths, DOS spectra and HOMO-LUMO plots.
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Jaiyong, Panichakorn. "Computational modelling of ligand shape and interactions for medicines design." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/computational-modelling-of-ligand-shape-and-interactions-for-medicines-design(28d49921-447f-4ea1-aaf2-aa764f45b2f2).html.
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Computational methods have been extensively developed at various levels of approximation in recent years to model biomolecular interactions and for rational drug design. This research work aims to explore the feasibility of using quantum mechanical (QM) methods within the two broad categories of in silico ligand-based and structure-based drug design. First, density functional theory at the M06L level of theory was employed to examine structure-activity relationships of boron-based heterocyclic compounds, anti-inflammatory inhibitors targetting the interleukin-1β (IL-1β) cytokine. Our findings from computed energies and shapes of the molecular orbitals provide understanding of electronic effects associated with the inhibitory activity. We also found that the boron atom, specifically its electrostatic polarity, appears to be essential for the anti-IL-1β activity as evidenced by the biological assay of non-boron analogues selected from the ligand-based virtual screening results. Secondly, we aimed to dock ligands at the active sites of zinc-containing metalloproteins with reasonable computational cost and with accuracy. Therefore, an in-house docking scheme based on a Monte Carlo sampling algorithm using the semiempirical PM6/AMBER force field scoring function was compiled for the first time within the Gaussian 09 program. It was applied to four test cases, docking to cytidine deaminase and human carbonic anhydrase II proteins. The docking results show the method’s promise in resolving false-positive docking poses and improving the predicted binding modes over a conventional docking scheme. Finally, semiempirical QM methods which include dispersion and hydrogen-bond corrections were assessed for modelling conformations of β-cyclodextrin (βCD) and their adsorption on graphene. The closed in vacuo βCD cccw conformer was found to be in the lowest energy, in good agreement with previous ab initio QM studies. DFTB3, PM6-DH2 and PM7 methods were applied to model the intermolecular interactions of large βCD/graphene complexes, over a thousand atoms in size. We found that the binding preference of βCD on graphene is in a closed conformation via its C2C3 rim, agreeing with reported experimental and computational findings.
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Tchernook, Ivan. "Strategies for Computational Investigation of Reaction Mechanisms in Organic and Polymer Chemistry Using Static Quantum Mechanics." Doctoral thesis, Universitätsbibliothek Chemnitz, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-198756.
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This thesis presents computational studies of problems in the organic and polymer chemistry. The state-of-the art quantum chemical methods are used to gain further insight into the origin and the nature of the reactions in three different organic and polymer systems. The research questions are conceptually approached by identifying the key aspects. Then an appropriate strategy for the quantum chemical modeling is developed.
In the scope of the polymer chemistry, the novel synthesis technique of nanostructured materials, the so-called twin polymerization, is investigated. Using three model systems of increasing complexity the influence of the anion (trifluoroacetate) in the reaction system is investigated. The effect of the solvent polarity as well as the effect of the entropic contributions are also considered.
The rearrangement reaction of the volatile cyanotritylcarbenes is another topic. These carbenes readily rearrange to ethene main products, however also small amount of the unexpected heptafulvenes is formed. This unprecedented heptafulvene formation is modeled in detail and the energetics is systematically evaluated to identify most reasonable rearrangement pathways of the probable multiple alternative routes. Computational investigation of other tritylcarbenes with varying spectator substituents results in sophisticated data base for experimental investigations.
At last, some controversial observations in experimental studies concerning the kinetics of the electrophilic alkylation of the barbiturate anion are studied. To interpret the kinetic measurements, different alkylation pathways are analyzed with respect to their energetics. Further, the influence of microsolvation is demonstrated.
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Matito, i. Gras Eduard. "Development, implementation and application of electronic structural descriptors to the analysis of the chemical bonding, aromaticity and chemical reactivity." Doctoral thesis, Universitat de Girona, 2006. http://hdl.handle.net/10803/7940.
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En la literatura sobre mecànica quàntica és freqüent trobar descriptors basats en la densitat de parells o la densitat electrònica, amb un èxit divers segons les aplicacions que atenyin. Per tal de que tingui sentit químic un descriptor ha de donar la definició d'un àtom en una molècula, o ésser capaç d'identificar regions de l'espai molecular associades amb algun concepte químic (com pot ser un parell solitari o zona d'enllaç, entre d'altres). En aquesta línia, s'han proposat diversos esquemes de partició: la teoria d'àtoms en molècules (AIM), la funció de localització electrònica (ELF), les cel·les de Voroni, els àtoms de Hirshfeld, els àtoms difusos, etc.L'objectiu d'aquesta tesi és explorar descriptors de la densitat basats en particions de l'espai molecular del tipus AIM, ELF o àtoms difusos, analitzar els descriptors existents amb diferents nivells de teoria, proposar nous descriptors d'aromaticitat, així com estudiar l'habilitat de totes aquestes eines per discernir entre diferents mecanismes de reacció.
In the literature, several electronic descriptors based in the pair density or the density have been proposed with more or less success in their pratical applications. In order to be chemically meaningful the descriptor must give a definition of an "atom" in a molecule, or instead be able to identify some chemical interesting regions (such as lone pair, bonding region, among others). In this line, several molecular partition schemes have been put forward: atoms in molecules (AIM), electron localization function (ELF), Voronoi cells, Hirshfeld atoms, fuzzy atoms, etc.
The goal of this thesis is to explore the density descriptors based on the molecular partitions of AIM, ELF and fuzzy atom, analyze the existing decriptors at several levels of theory, propose new aromaticity descriptors, and study its ability to discern between different mechanisms of reaction.
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Toliautas, Stepas. "Elektroninio sužadinimo procesai fotoaktyviose organinėse molekulėse." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2014. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2014~D_20140929_100514-01959.
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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.
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Toliautas, Stepas. "Electronic excitation processes of photoactive organic molecules." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2014. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2014~D_20140929_100526-37294.
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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.
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"Molecular Design for Nonlinear Optical Materials and Molecular Interferometers Using Quantum Chemical Computations." Diss., 2009. http://hdl.handle.net/10161/1205.
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Xiao, Dequan. "Molecular Design for Nonlinear Optical Materials and Molecular Interferometers Using Quantum Chemical Computations." Diss., 2009. http://hdl.handle.net/10161/1205.
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Quantum chemical computations provide convenient and effective ways for molecular design using computers. In this dissertation, the molecular designs of optimal nonlinear optical (NLO) materials were investigated through three aspects. First, an inverse molecular design method was developed using a linear combination of atomic potential approach based on a Hückel-like tight-binding framework, and the optimizations of NLO properties were shown to be both efficient and effective. Second, for molecules with large first-hyperpolarizabilities, a new donor-carbon-nanotube paradigm was proposed and analyzed. Third, frequency-dependent first-hyperpolarizabilities were predicted and interpreted based on experimental linear absorption spectra and Thomas-Kuhn sum rules. Finally, molecular interferometers were designed to control charge-transfer using vibrational excitation. In particular, an ab initio vibronic pathway analysis was developed to describe inelastic electron tunneling, and the mechanism of vibronic pathway interferences was explored.
Dissertation
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Faglioni, Francesco. "Quantum chemical computations of heterogeneous selective oxidation, STM images, and multiple bond reactions." Thesis, 1998. https://thesis.library.caltech.edu/5313/1/Faglioni_f_1998.pdf.
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Chapter one of this thesis describes first principles electronic structure computations performed to understand the mechanism of molecular oxygen activation by vanadyl pyrophosphate. The process is believed to play a key role in the catalytic oxidation of n-butane to maleic anhydride. The results obtained demonstrate that the mechanism involves at least two layers of vanadyl pyrophosphate crystal. Based on the computed energetics for small clusters, we propose an activation mechanism which involves the transfer of one oxygen atom from the first to the second layer of the crystal concerted with dioxygen activation by the first layer.
Chapter two describes a novel ab-initio computational technique, called GVB-RCI, which correctly describes the stretching and dissociation of multiple bonds and provides smooth potential energy surfaces for most chemical reactions. The technique is a special case of Multi Configuration SCF that does not have the Perfect Pairing restriction and still scales well with the size of the system. The capabilities and limitations of GVB-RCI are illustrated in the case of a few simple chemical reactions.
Chapter three contains a theoretical model describing the Scanning Tunneling Microscopy (STM) imaging of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort, and provides images that are in qualitative agreement with experimental results. The model predicts that topographic effects will dominate the STM images of alkanes on graphite surfaces. The computations correlate well with the STM data of functionalized alkanes, and allow assessment of the structure and orientation of most of the functionalized alkanes
that have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals of the adsorbed molecules, may play an important role in determining the STM
image contrast of such systems.
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Liu, Fan. "Classical Force Field Simulations of Biological Processes and Quantum Chemical Computations of Homogeneous Catalysts." Thesis, 2016. https://thesis.library.caltech.edu/9849/7/FanLiu2016thesis.pdf.
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Computational chemistry methods and tools have enabled studies of biological processes and chemical reactions to get insights from detailed atomic structures and reaction mechanisms. In this thesis, two biological problems are attacked by the classical force fields simulations and two homogeneous catalysis problems are studied by quantum chemical calculations. In all four problems, new insights have been revealed by the computational results.
Chapter 1 briefly reviews the computational chemistry theories and methods developed and popularized in the past few decades. Chapter 2 addresses the protein-protein interaction problem in the onset of meningitis where E. coli OmpA interacts with FcγRI α-chain (FcγRIa) to invade macrophages. Computationally predicted three-dimensional structure of the OmpA-FcγRIa complex showed the role of three N-glycans in FcγRIa in the interaction. Chapter 3 studies the molecular origin of the bitter aftertaste of a kind of natural sweetener called steviol glycosides. By examining the predicted binding complexes between the human bitter taste receptors 2R4 and 2R14 which could be activated by steviol glycosides, a general activation model is proposed to explain the structure-function relationship and to predict new natural sweeteners with less bitterness. Chapter 4 investigated the reaction mechanisms of methane to methanol conversion by a biomimetic tricopper cluster compound. An unusual exchange-stabilized multiradical state is found to be responsible for the hydrogen abstraction reactivity and a methyl radical rebound mechanism is proposed for methane oxidation. Calculations also show interesting spin crossing during the reaction cycle with high spin state forbidden for methyl rebound. Chapter 5 examines the reaction mechanisms in olefin hydrosilylation by the Pt-based Karstedt’s catalyst. An unexpected rate-determining step of agostic bond dissociation is found in between the elementary reaction steps proposed previously. The regioselectivity of the products are studied. An alternative reaction cycle which is kinetically unflavored is proposed. Oxygen stability is studied.
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Rotem, Karin. "Computational quantum chemistry applied to nitrogen oxide chemistry and new fire-resistant polymers." 1999. https://scholarworks.umass.edu/dissertations/AAI9920647.
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Computational quantum chemistry was used as a tool to predict needed thermochemistry and kinetics for two classes of problems: formation and destruction of NOx pollutants and development of new fire-resistant polymers. Of the latter, polycarbodiimides and polyhydroxyamides (PHA's) were studied. Different methods were used: HF/6-31 G(d), BAC-MP4 (bond-additivity corrections to UMP4 energies and HF vibrational frequencies), PM3 semi-empirical, and combinations. On the NOx problem, work focused on using theory to generate improved kinetics in H2/O2/NOx combustion. The results were a set of thermochemical data and highpressure-limit kinetics for NOx formation and destruction. Hartree-Fock structures and frequencies and fourth-order Moeller-Plesset energies were used for reactions of H/N/O-species involving H1N1O1 , N1O2, N2O1, H1N 2O1, and N2O2 surfaces, including NH + NO ↔ N2O + H, N2O + O ↔ NO + NO, N + OH ↔ NO + H, N + O2 ↔ NO + O, and N + NO ↔ N2 + O. Thermochemical results were discussed in the form of potential energy surfaces. In general, BAC-MP4 heats of formation compared consistently well to literature data. The results generated from this work allowed evaluation of pressure-dependent kinetics and, ultimately, a refined group of reactions for the NOx mechanism. Strengths of particular bonds and bonding combinations in polycarbodiimides were calculated. Work focused on effects of R groups, chain size and stereoregularity on bond dissociation energies (BDE). Specifically, five polycarbodiimide systems were studied: (1) R=R′=H, (2) R=R′ =CH3, (3) R=R′=CH2CH 3, (4) R=CH(CH3)(Phenyl), R′=H, and (5) R=CH(CH3)(phenyl), R′=CH 3. Methyl- and ethyl-substituted polycarbodiimides decreased the bond strength of the central C-N bond. Ligands on the amine (backbone) nitrogen weakened its chain C-N bond dramatically. However, a lower barrier reaction has also been identified. Results imply rapid, concerted unzipping of this polymer, a result consistent with experiment. For the polyhydroxyamide (PHA) system, a model cyclization reaction of PHA to polybenzoxazole (PBO) was evaluated. PHA cyclization to PBO has been studied experimentally, but a detailed theoretical reaction surface has never been evaluated. Moreover, a plausible mechanism by which PHA arrives at PBO had not been previously determined. The calculated overall heat of reaction was thermoneutral, and decomposition was determined to occur at 212°C, compared to the 215°C experimental value. The hydrogen-transfer reaction and a four-center concerted transition-state reaction were found to be the limiting steps.
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Ali, H. R. H., Howell G. M. Edwards, John Kendrick, Tasnim Munshi, and Ian J. Scowen. "An experimental and computational study on the epimeric contribution to the infrared spectrum of budesonide." 2010. http://hdl.handle.net/10454/4620.
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NoBudesonide is a mixture of 22R and 22S epimers. The epimeric content of budesonide was reported in both British and European pharmacopoeias to be within the range of 60-49/40-51 for R and S epimers, respectively. In this work, contribution of the two epimers to the overall infrared spectrum of budesonide has been investigated by quantum chemical calculations.
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Coley, Terry Ronald. "Prediction of scanning tunneling microscope images by computational quantum chemistry: chemical models and software design." Thesis, 1993. https://thesis.library.caltech.edu/5310/1/Coley_tr_1993.pdf.
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We have created chemical models for predicting and interpreting STM images of several specific systems. Detailed studies are made of transition metal dichalcogenides (MoS_2 and MoTe_2), Xe on Ni (110), C_3H_4 on Ni (110) and n-butyl benzene on a graphite model (C_(42)O_6H_(12). In the case of MoS_2 we study the ambiguity in the STM images regarding the assignment of peaks to the subsurface metal or the surface chalcogenide. In the Ni models we study STM imaging mechanisms for cases where the adsorbate states lie far above and below the metal Fermi level. The large n-butyl on graphite system models a system where adsorbate states can play a direct role in the imaging. Results from the cluster studies are related to various STM imaging modes, including constant current mode, constant height mode, and barrier height imaging.
Two new procedures are developed to aid in computational prediction of STM images. First, we implement an algorithm for computing Bardeen-type tunneling matrix elements from ab initio wave functions in Gaussian basis sets. Second, we show how to obtain state densities as a function of energy for bulk substrate/adsorbate systems using only Fock matrix elements from cluster calculations. Initial results are presented for a linear chain of Ni atoms with a perturbing Xe atom.
A software environment for computational chemistry developed in the course of performing these calculations is presented. Tools for creating computational servers to perform chemistry calculations are described. Embedded in each chemistry server is a public domain control language created by J. Ousterhout at the University of California, Berkeley. This allows the development of a variety of clients for controlling the servers using a common language. Clients can be simple text "scripts" that organize a calculation, graphical interfaces, or control streams from other programs. All software entities are designed in an object oriented fashion discussed in the text.
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Gregory, Kasimir Phennah. "A quantum chemical investigation of Hofmeister effects in non-aqueous solvents." Thesis, 2022. http://hdl.handle.net/1959.13/1460595.
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Research Doctorate - Doctor of Philosophy (PhD)Specific ion effects (SIEs) encompass any phenomenon induced by ions that is dependent on the identity of the ions, and not just their charge or concentration. These occur in salts, electrolyte solutions, ionic liquids, acids and bases and have been known for over 130 years, from which the Hofmeister series originated. They are important in biology, nutrition, electrochemistry and various interfacial or geophysico-phenomena. It is perhaps harder to find a “real-world” system in which specific ion effects don’t occur, than systems where they do. Nonetheless, despite such ubiquity and effect on our daily lives, our understanding of these salty solutions is limited. This thesis addresses the knowledge gap surrounding the lack of parameters (for both ion and solvent) for quantifying SIEs in aqueous and nonaqueous environments. This thesis begins with a deeper introduction to the topic of SIEs and highlights the current state-of-play. The theories underlying quantum mechanics and computational chemistry are discussed to highlight how they may be applied to elucidate some of the fundamental origins of SIEs. These methods were subsequently used to investigate possible energetic origins of counterion and solvent induced reversals to the Hofmeister series, and highlights that the Lewis acidity and basicity (collectively Lewis strength) indices of the cations and anions respectively, can quantify SIEs. Following this revelation, these empirical parameters were recast in terms of intermolecular forces. Electrostatics appeared to govern the Lewis strength indices, so these were replaced with an electrostatic parameter, ϸ (“sho”), that originates from Coulomb’s Law. For anions, ϸ is shown to quantify SIE trends observed in enthalpies of hydration, polymer lower critical solution temperatures, enzyme and viral activities, SN2 reaction rates and Gibbs free energies of transfer from water to nonaqueous solvents highlighting the versatility of ϸ as a new SIE parameter. Cation interactions are more prone to deviations from ϸ correlations. In the absence of any cosolute (i.e., pure ion-solvent interactions) however, cation solvent interactions follow a strong trend with Coulomb’s Law for ~15 different solvents. This supports a conclusion that competing electrostatic interactions between the solvent and a cosolute for the cation may mask each other allowing non-electrostatic contributions to play a dominant role. Furthermore, with similarity to the ion parameterisation, the ϸ values at the negative and positive solvent dipolar atoms correlate with the solvent’s Lewis basicity and acidity respectively. Additionally, these analyses can be related to macroscopic solvent parameters such as the relative permittivity. The data deficiency issue facing the SIE field was more generally addressed in this thesis by the generation of IonSolvR, a repository containing over 3000 distinct QM/MD trajectories of up to 52 ions in 28 bulk solvents on nanosecond-scales. Finally, the key findings of this thesis are summarised and an outlook on the field of SIEs and the broader implications arising from this thesis is presented.
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Pramanik, Chirantan. "Ab initio Quantum Chemical Studies on Kinetic Fractionation during the analysis of Carbonates for the Clumped Isotope Thermometry." Thesis, 2021. https://etd.iisc.ac.in/handle/2005/5214.
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Stable and clumped isotopic compositions of molecules and minerals carry the signatures of temperatures and other physical and chemical conditions of the time of their formation. Isotopic compositions of such precipitate are preserved in carbonate that provides information about the climate through geological time. The carbonates formed in the aquatic environment serve as an archive for past climate and temperature reconstruction. In nature, sedimentary carbonate rocks are primarily composed of minerals calcite (CaCO3) and dolomite (CaMg(CO3)2). They comprise ~20% of the surface sedimentary rocks on Earth and are also found in other planets, with the oldest being ~3.5 Ga, almost as primitive as the Earth itself. The majority of them form in the aquatic environments that ranged from the warm, sunlit shallow seafloor to the cold, perpetually dark, deep ocean. Carbonate rocks are also traced in the terrestrial and extraterrestrial environment, which includes terrestrial spring waters, rivers and lakes, caves, soils, and meteorites from outer space.
Ab initio quantum chemical simulations are used to calculate the extent of equilibrium and kinetic isotope fractionations, which provided additional theoretical references in clumped isotope paleothermometry. Ab initio quantum chemical simulations provide the inputs in terms of vibration frequencies and thermal energies of the optimized stable molecules and the transition state structures for the partition function calculations of equilibrium and kinetic fractionations. Ab initio calculations using density functional theory (DFT) are performed using 'Gaussian09' computational chemistry packages. Equilibrium constant and partition function calculations are performed using scripts in Matlab and Python.
Though the clumped isotope proxy is based on the temperature dependence of 13C-18O bonding preference in the mineral lattice, which is captured in the product CO2, there is limited information on the phosphoric acid reaction mechanism and the magnitude of clumped isotopic fractionation (mass 63 in CO32- to mass 47 in CO2) during the acid digestion. We explored the reaction mechanism for phosphoric acid digestion of calcite using first-principles density functional theory. We identified the transition state structures for each protonation reaction involving different isotopologues and used the corresponding vibrational frequencies in reduced partition function theory to estimate Δ47 acid fractionation. We showed that the acid digestion reaction, which results in the formation of CO2 enriched with 13C-18O bonds, commences with the protonation of calcium carbonate in the presence of water. Our simulations yielded a relationship between Δ47 acid fractionation for calcite and reaction temperature as Δ47 acid fractionation in calcite = -0.30175 + 0.57700*105/ T2 - 0.10791* (105/ T2)2, with T varying between 298.15 K and 383.15 K. This relationship shows a higher slope (Δ47 acid fractionation vs. 1/T2 curve) than previous studies based on the H2CO3 model. The theoretical estimates from the present and earlier studies encapsulate experimental observations from both 'sealed vessel' and 'common acid bath' acid digestion methods from literature.
Previous theoretical models for determining clumped isotopic fractionation in product CO2 during acid digestion of carbonates are independent of the cations present in the carbonate lattice. Hence further study is required to understand the cationic effect. We studied the acid reaction mechanism and calculated the acid fractionation factor for dolomite using partition functions and vibrational frequencies obtained for the transition state structure, and determined the effect of cations on the acid fractionation factor. Theoretically obtained acid fractionation factor for dolomite can be expressed as Δ47 acid fractionation in dolomite = -0.28563 + 0.49508*(105/ T2) - 0.08231* (105/ T2)2 for a temperature range between 278.15 K and 383.15 K. The theoretical slope of the dolomite-acid digestion curve is lower than that of the calcite-acid digestion curve obtained using the identical reaction mechanism. Our theoretical slope is consistent with the result from the common acid bath experiments but higher than the slope obtained in the experimental study using the sealed vessel and modified sealed vessel method and previous theoretical study using the H2CO3 model. Transition state structure, obtained in our study, includes the cations present in the carbonate minerals and provides distinct acid fractionation factors for calcite and dolomite. The observed gentler slope of theoretically calculated dolomite-acid digestion curve compared to calcite is expected considering the stronger Mg-O bond.
In the present theoretical study, we provided the acid digestion reaction mechanism based on the protonation and determined a quantitative acid digestion correction factor for a range of reaction temperature for the experimental protocols where the product CO2 is immediately removed from the system, and there is not enough chance of post-digestion isotope exchanges. We suggest using appropriate acid digestion correction factors depending on the experimental techniques used for acid digestion of carbonates.CSIR-UGC NET JRF & SRF Fellowship
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Huzayyin, Ahmed. "Effect of Chemical Impurities on the Solid State Physics of Polyethylene." Thesis, 2011. http://hdl.handle.net/1807/31787.
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Computational quantum mechanics in the frame work of density functional theory (DFT) was used to investigate the effect of chemical impurities on high field conduction in polyethylene (PE). The impurity states in the band gap caused by common chemical impurities were characterized in terms of their “depth”, i.e. energy relative to their relevant band edge (valence band or conduction band), and in terms of the extent to which their wavefunctions were localized to a single polymer chain or extended across chains. It was found that impurity states can affect high field phenomena by providing “traps” for carriers, the depths of which were computed from first principle in agreement with estimates in literature. Since the square of the wavefunction is proportional to the spatial electron probability density, transfer of charge between chains requires wavefunctions which are extended across chains. Impurity states which are extended between chains can facilitate the inherently limited interchain charge transfer in PE, as the DFT study of iodine doped PE revealed.
The introduction of iodine into PE increases conductivity by several orders of magnitude, increases hole mobility to a much greater extent than electron mobility, and decreases the activation energy of conduction from about 1 eV to about 0.8 eV. These characteristics were explained in terms of the impurity states introduced by iodine and wavefunctions of those states. Understanding the effect of iodine on conduction in PE provided a basis for understanding the effect of common chemical impurities on conduction therein. In particular, carbonyl and vinyl impurities create states which should promote hole mobility in a manner very similar to that caused by iodine. It was demonstrated that in the context of high field conduction in PE, besides the traditional focus on the depth of impurity states, it is important to study the spatial features of the states wavefunctions which are neither discussed nor accounted for in present models.
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Summoogum, Sindra Lutchmee. "Studies on the oxidative and non-oxidative decomposition of alpha-cypermethrin and related molecules of non-chlorinated biphenyl and dibenzo-p-dioxin." Thesis, 2012. http://hdl.handle.net/1959.13/932043.
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Research Doctorate - Doctor of Philosophy (PhD)In this thesis, we have investigated the thermal decomposition of the pyrethroid, alpha-cypermethrin, and two cognate molecules of biphenyl and dibenzo-p-dioxin (DD), into toxic products including polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F, dioxins). Alpha-cypermethrin has widespread indoor and outdoor applications while biphenyl is mostly used as a fungicide and termiticide. Based on these results, a mechanism has been developed in which the key reaction steps occurring during pyrolysis and oxidation of alpha-cypermethrin are outlined. With the aim of gaining better and more comprehensive understanding of the formation of PCDD/F and destruction of DD, we examined a range of reaction conditions using a bench type tubular reactor facility, with particular focus on varying oxygen levels, temperatures and residence times. Stable reaction products were identified and quantitated using a range of analytical techniques and equipment, including micro gas chromatograph (µGC), triple quadrupole mass spectrometer (QQQMS), ion trap mass spectrometer (ITMS), and Fourier transform infrared (FTIR) spectrometer. For some key reaction steps, density functional theory (DFT) calculations were deployed to help unravel the reaction mechanism. Initially, we studied the pyrolysis of alpha-cypermethrin in the temperature range of 300 to 600 °C. We identified five main gaseous species including hydrogen chloride, hydrogen cyanide, methyl cyanide, acetaldehyde and crotonaldehyde. We identified two major pathways, one at low temperatures (two species form only at 450 °C) and the other at higher temperatures (formation of naphthalene and ethylbenzene, possibly by reaction with radicals, expulsion of CO and internal rearrangement, rather than by breaking of ether bridges). The unimolecular rearrangement of alpha-cypermethrin was observed at low temperatures, dominating over the alternative pathway which involves the recombination of the initial products. To gain further understanding of this pathway, we performed DFT computations, at the B3LYP/6-31G(d) level of theory, to understand the role of the CN group in O-CH(CN) bond fission in alpha-cypermethrin, in comparison to fission of the same bond in permethrin. There is a significant lowering of the bond energy which is due to considerable stabilisation of the CH(CN)C₆H₅ radical compared with the benzyl radical formed in the permethrin model case. Consequently, the activation energy for O—CHCN fission in cypermethrin is relatively similar to the activation energy for internal rearrangement and aromatisation. Hence, bond fission in alpha-cypermethrin should predominate at a much lower temperature than in permethrin itself, exactly as observed in the present experiments. The oxidative pyrolysis of alpha-cypermethrin generates substantially more PCDF than PCDD under all experimental conditions (temperatures, residence times and equivalence ratio), with the maximum emission factor of PCDD/F being observed at 550 °C, a residence time of 5 s and an equivalence ratio of 0.03. As indicated by the homologue distribution of PCDD/F, all the chlorinated congeners were detected with the exception of octachlorinated dibenzo-p-dioxins and octachlorinated furans (OCDD/F) in our measurements. The VOC analysis revealed the production of benzene, phenol, chlorotoluenes, trichlorophenols, tetrachlorophenols. The formation of PCDD/F from the gas-phase oxidation of alpha-cypermethrin may proceed through the coupling of chlorophenoxy radicals to benzene or chlorinated benzenes, and the self-condensation of chlorophenoxy radicals. This study combines the results of experimental measurements and theoretical computations to investigate the initial steps in the oxidation of dibenzo-p-dioxin (DD). The analyses of VOC, performed on a high resolution gas chromatograph-triple quadrupole mass spectrometer (HRGC-QQQMS), identified 2-methylbenzofuran and 2,3-dihydro-2-methylenebenzofuran as the initial products. This has been confirmed by injection of authentic standards and the application of collision induced dissociation that fragmented the isolated parent ions into specific product ions affording the identification of parent species. The oxidative decomposition of DD initiated at around 450 °C, with the evolution of VOC being maximum between 650 and 700 °C. At temperatures in excess of 750 °C, all VOCs were completely oxidised. The potential energy surface, based on the density functional theory of B3LYP, mapped the initial steps involved in the oxidation of DD, and yielded a detailed reaction scheme for the onset of oxidation of DD that results in the formation of 2-methylbenzofuran and 2,3-dihydro-2-methylenebenzofuran. Finally, we discuss the feasibility of the oxidation of biphenyl at low temperatures. Although it has been known for several years that combustion of polychlorinated biphenyl (PCB) in accidental fires of electrical equipment and in municipal waste can lead to significant emissions of dioxins, understanding of the mechanism of the oxidation process is quite limited. Oxidation of biphenyl (as a prototype model compound for PCB) in an alumina reactor at 490 ºC yields the initial products dibenzofuran and benzaldehyde which have been confirmed in GC/MS studies. It is postulated that O₂ (¹Δg) whose formation is catalysed by the reactor surfaces, initiates the reaction at this relatively low temperature. Quantum chemical computations of the reaction potential energy surfaces suggest low energy pathways to the observed initial products.
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Kabanda, Mwombeki Mwadham. "Computational study of the molecules of selected acylated phloroglucinols in vacuo and in solution." Thesis, 2012. http://hdl.handle.net/11602/67.
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(11190201), Jacob R. Milton. "ION-MOLECULE REACTIONS STUDIED BY USING DENSITY FUNCTIONAL THEORY CALCULATIONS AND MASS SPECTROMETRY FOR SATURATED HYDROCARBON ANALYSIS AND THE STUDY OF ORTHO- AND PARA-PYRIDYNES." Thesis, 2021.
Find full textAbstract:
The work described herein is related to gas-phase ion-molecule reactions studied by using mass spectrometry. Chapter 2 describes density functional theory, a method used in chapters 4 and 5 to propose reaction mechanisms for reactions previously observed by others by using mass spectrometry. Chapter 3 describes a study that demonstrates that the fragmentation of saturated hydrocarbons occurs due to proton-transfer reactions that occur between these species and protonated molecules generated from molecules present in air such as nitrogen and water. Saturated hydrocarbons are studied in a wide variety of fields, and better methods to analyze complex mixtures of these compounds would facilitate their analysis. Chapter 4 discusses mechanisms of reactions for previously studied ion-molecule reactions of pyridynes studied by others by using mass spectrometry. Reactions of pyridynes are important to study arynes have been previously used in organic synthesis, and pyridine moieties are particularly common in biological compounds. Chapter 5 discusses density functional theory calculations used to determine why some organic polyradical undergo hydride abstractions from cyclohexane while others do not. The study discusses reactions taking place between both singlet and triplets states of the 2,5-didehydropyridinium cation and cyclohexane as a model, which are compared to reactions of the 2-pyridyl cation and 2-dehydropyridinium cation with cyclohexane. These studies may help improve our understanding of the reactivity-controlling factors of organic polyradicals, which may help improve toxic drug candidates like cytostatic enediynes.