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1
Gkionis, Konstantinos. "Quantum chemical studies of metal-DNA interactions." Thesis, Cardiff University, 2010. http://orca.cf.ac.uk/55045/.
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A series of density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) calculations are used to investigate the binding of platinum and ruthenium anticancer drugs to DNA. The qualitative and quantitative features of Becke's half-and-half (BHandH) functional for calculating geometries, binding energies and harmonic frequencies of non- covalently bound systems are tested and the intermolecular interactions are characterised and quantified using the QTAIM electron densities. Application of this DFT-QTAIM approach to complexes of the type (n6-arene)Ru(en)(nucleobase) 2+ shows a clear preference for binding at guanine over any other base both in gas phase and in aqueous solution, a trend explained on the basis of QTAIM and molecular orbital data. Key parameters of the QM/MM methodology within the ONIOM scheme and efficient geometry optimisation strategies are examined for applications involving DNA oligonucleotides. Calculations on cis- Pt(NH3)2 2+ (cisplatin) bound to d(CpCpTpGpGpTpCpC).(GpGpApCpCpApGpG) reveal that proper consideration of the electrostatics between the QM an MM regions can lead to acceptable geometries, especially when explicit solvent molecules are present. This approach is used to explore the effects of methyl substitution on the binding of a series of Pt(en)2+ (en: ethylenediamine) complexes to dinucleotides. Among the examined methyl derivatives, significant differences are observed for the variants whose en nitrogen atoms are multiply methylated. Binding energies are found to be in excellent correlation with in vitro cytotoxicity data expressed as -log(IC5o). The above mentioned cisplatin-oligonucleotide complex is compared against three clinically approved platinum drugs (carboplatin, heptaplatin and lobaplatin). Calculations on truncated models show a stronger binding for cisplatin among the four complexes and numerous intermolecular interactions are located via QTAIM analysis in the lobaplatin and heptaplatin complexes. Additionally, subtle differences in key geometrical parameters are observed among the complexes around the sites of platination, with the exception of unusually short interplanar base - base distances in the complexes of loba- and heptaplatin. Finally, the same QM/MM methodology is applied to oligonucleotide sequences of five base pairs that contain difluorotoluene or mismatched base pairs, which are shown to be too flexible to be optimised at reliable structures at the chosen level of truncation. Comparisons among obtained structures using different input parameters further validate the followed QM/MM approach.
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Katukuri, Vamshi Mohan. "Quantum chemical approach to spin-orbit excitations and magnetic interactions in iridium oxides." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-160735.
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In the recent years, interest in TM oxides with 5d valence electrons has grown immensely due to the realization of novel spin-orbit coupled ground states. In these compounds, e.g., iridates and osmates, the intriguing situation arises where the spin-orbit and electron-electron interactions meet on the same energy scale. This has created a new window of interest in these compounds since the interplay of crystal field effects, local multiplet physics, spin-orbit couplings, and intersite hopping can offer novel types of correlated ground states and excitations. In 5d5 iridates, a spin-orbit entangled j = 1/2 Mott insulating state has been realized recently. A remarkable feature of such a ground state is that it gives rise to anisotropic magnetic interactions. The 2D honeycomb-lattice 213 iridium oxides, A2IrO3 (A=Li,Na), have been put forward to host highly anisotropic bond-dependent spin-spin interactions that resemble the Kitaev spin model, which supports various types of topological phases relevant in quantum computing. The 2D square-lattice 214 iridates Sr2IrO4 and Ba2IrO4 are, on the other hand, appealing because of their perceived structural and magnetic simi- larity to La2CuO4, the mother compound of the cuprate high-Tc superconductors. This has promoted the latter iridium oxide compounds as novel platforms for the search of high-Tc superconductivity.
To put such considerations on a firm footing, it is essential to quantify the different coupling strengths and energy scales, as they for instance appear in effective Hamiltonian descriptions of these correlated systems. Moreover, it is important to correctly describe their effects. In this thesis, the electronic structure and magnetic properties of 5d5 (mainly 214 and 213) iridates are studied using wave-function-based quantum chemistry methods. These methods are fully ab initio and are capable of accurately treating the electron-electron interactions without using any ad hoc parameters. The spin-orbit entangled j = 1/2 ground state in 214, 213 and other lower symmetry Sr3CuIrO6 and Na4Ir3O8 iridates is first analyzed in detail, by studying the local electronic structure of the 5d5 Ir4+ ion. We establish that the longer-range crystal anisotropy, i.e., low-symmetry fields related to ionic sites beyond the nearest neighbor oxygen cage, strongly influence the energies of Ir d levels. The ground state in all the compounds studied is j = 1/2 like with admixture from j ≃ 3/2 states ranging from 1 – 15 %. Further, the average j ≃ 1/2 → j ≃ 3/2 excitation energy we find is around 0.6 eV.
The NN magnetic exchange interactions we computed for 214 iridates are predominantly isotropic Heisenberg-like with J ~ 60 meV, 3 – 4 times smaller than found in isostructural copper oxides. However, the anisotropic interactions are an order of magnitude larger than those in cuprates. Our estimates are in excellent agreement with those extracted from experiments, e.g., resonant inelastic x-ray scattering measurements. For the 213 honeycomb-lattice Na2IrO3 our calculations show that the relevant spin Hamiltonian contains further anisotropic terms beyond the Kitaev-Heisenberg model. Nevertheless, we predict that the largest energy scale is the Kitaev interaction, 10 to 20 meV, while the Heisenberg superexchange and off-diagonal symmetric anisotropic couplings are significantly weaker. In the sister compound Li2IrO3, we find that the structural inequivalence between the two types of Ir-Ir links has a striking influence on the effective spin Hamiltonian, leading in particular to two very different NN superexchange pathways, one weakly AF (~ 1 meV) and another strongly FM (−19 meV). The latter gives rise to rigid spin-1 triplets on a triangular lattice.
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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.
4
Sure, Rebecca [Verfasser]. "Evaluation and Development of Quantum Chemical Methodologies for Noncovalent Interactions and Supramolecular Thermochemistry / Rebecca Sure." Bonn : Universitäts- und Landesbibliothek Bonn, 2016. http://d-nb.info/1096329867/34.
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ALESSANDRINI, Silvia. "Modelling Weak Interactions in the Gas Phase: From Rotational Spectroscopy to Reaction Rates Using Accurate Quantum-Chemical Approaches." Doctoral thesis, Scuola Normale Superiore, 2022. http://hdl.handle.net/11384/124922.
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During these four years of PhD, my research was focused on structural, energetic
and spectroscopic characterisation of stable and reactive systems in the gas phase. A
special focus has been put on the theoretical description of non-covalent interactions
(NCIs) as they occur in the gas phase. The interest on these chemical bonds arises from
the fact that they play a key role in many aspects of life. Indeed, they are responsible for
the folding of proteins and characterise the shape of DNA and RNA. The same types of
interactions drive self-assembling processes and the interaction between a receptor and
its ligands. Furthermore, NCIs can influence chemical reactions by favouring one conformer
with respect to others in a given pathway and they can also affect the structure
of reactive intermediates and transition states. Usually, these phenomena are not due
to a single interaction but to the sum of several hundreds (or thousands) non-covalent
contacts occurring simultaneously and in a cooperative manner. Therefore, it is rather difficult to elucidate the type of interactions occurring and their effects on the molecular
structures involved. However, one can aim at studying models of such weak bonds
through the analysis of prototypical single NCIs occurring in an isolated environment.
This idea can be exploited thanks to experimental methods based on rotational spectroscopy,
which is an intrinsic high-resolution technique working exclusively in the
gas phase, but also thanks to quantum chemistry. Rotational spectroscopy can unveil
the interaction occurring in a binary system where two molecules interact and it is able
to point out the effects of non-covalent interactions on the molecular structures of the
fragments involved. On the other hand, quantum chemical simulations allow for: (i)
exploration of the potential energy surface (PES) of the bimolecular system, thus identifying
all the possible isomers that can arise from the contacts of two fragments, also in the case of reactive PESs; (ii) accurate energetic studies and decomposition of the
energy to unveil the nature of the interaction; (iii) providing ab initio data useful to
guide the interpretation of experimental spectra, which can be difficult to analyse due
to several factors. Currently, state-of-the-art information on non-covalent complexes
are obtained via a strong interplay of rotational spectroscopy and quantum chemistry.
However, computational simulations show some limitations due to the challenge of
accurately describing NCIs; indeed, they are extremely sensitive to the level of theory
employed and an effective compromise between accuracy and computational cost is always difficult. In this context, my PhD thesis aimed at developing accurate computational
models to treat medium-sized systems (20-30 atoms) dominated by NCIs
such as intermolecular (binary) complexes in the gas phase, to support and/or complement
experimental rotational spectroscopy, as well as reactive intermediates and
transition states, to accurately describe reaction pathways. The developed models are
able to provide reliable estimates for both energies and geometries. These approaches
are based on coupled-cluster techniques including single and double excitations and
a perturbative treatment of triples (CCSD(T) method). To reduce the computational
cost without degrading the accuracy, the CCSD(T) method is employed in conjunction
with Møller-Plesset perturbation theory to the second order (MP2) to account for the
extrapolation to the complete basis set (CBS) limit and the core-valence correlation effects.
Standard methods and their explicitly correlated counterparts, i.e., CCSD(T)-F12
and MP2-F12, have been employed. The thesis will describe how these new computational
models have been built based on accurate reference data reported in the literature
and the fundamental role played by diffuse functions in the basis sets. Then, the focus will move on the discussion of several examples where the new computational
models, namely junChS and junChS-F12, have been used to characterise energies
and structures of non-covalent complexes such as the complex between sulfur dioxide
and dimethyl sulfide (SO2-DMS), the benzofuran-formaldehyde complex (C8H6OH2CO),
and the trifluoroacetophenone-water (CF3COC6H5 –H2O) complex. The thesis
will also address the performances of the junChS model in the case of astrochemically
relevant reaction pathways, where the energetic barriers play a key role in establishing
reliable reaction rate coefficients. Also in this case, a few examples will be given
considering the reactions between methanimine (CH2NH) and the CP radical, between
oxirane (c-C2H4O) and the CN radical, and between propene (C3H6) and the C3N radical.
In these cases, the developed models had to provide accurate energies, not only
for closed-shell species (all paired electrons), but also for structures with an unpaired
electron (doublet state, open-shell), which are troublesome electronic configurations to describe from the theoretical point of view.
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Kleimaier, Dennis [Verfasser], and Lothar [Akademischer Betreuer] Schad. "Exploring Protein Interactions with 23Na Triple-quantum MRS and 1H Chemical Exchange Saturation Transfer MRI / Dennis Kleimaier ; Betreuer: Lothar Schad." Heidelberg : Universitätsbibliothek Heidelberg, 2021. http://d-nb.info/1227155832/34.
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Kleimaier, Dennis [Verfasser], and Lothar R. [Akademischer Betreuer] Schad. "Exploring Protein Interactions with 23Na Triple-quantum MRS and 1H Chemical Exchange Saturation Transfer MRI / Dennis Kleimaier ; Betreuer: Lothar Schad." Heidelberg : Universitätsbibliothek Heidelberg, 2021. http://nbn-resolving.de/urn:nbn:de:bsz:16-heidok-293608.
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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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Bandyopadhyay, Avra Sankar. "Light Matter Interactions in Two-Dimensional Semiconducting Tungsten Diselenide for Next Generation Quantum-Based Optoelectronic Devices." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1752376/.
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In this work, we explored one material from the broad family of 2D semiconductors, namely WSe2 to serve as an enabler for advanced, low-power, high-performance nanoelectronics and optoelectronic devices. A 2D WSe2 based field-effect-transistor (FET) was designed and fabricated using electron-beam lithography, that revealed an ultra-high mobility of ~ 625 cm2/V-s, with tunable charge transport behavior in the WSe2 channel, making it a promising candidate for high speed Si-based complimentary-metal-oxide-semiconductor (CMOS) technology. Furthermore, optoelectronic properties in 2D WSe2 based photodetectors and 2D WSe2/2D MoS2 based p-n junction diodes were also analyzed, where the photoresponsivity R and external quantum efficiency were exceptional. The monolayer WSe2 based photodetector, fabricated with Al metal contacts, showed a high R ~502 AW-1 under white light illumination. The EQE was also found to vary from 2.74×101 % - 4.02×103 % within the 400 nm -1100 nm spectral range of the tunable laser source. The interfacial metal-2D WSe2 junction characteristics, which promotes the use of such devices for end-use optoelectronics and quantum scale systems, were also studied and the interfacial stated density Dit in Al/2D WSe2 junction was computed to be the lowest reported to date ~ 3.45×1012 cm-2 eV-1.
We also examined the large exciton binding energy present in WSe2 through temperature-dependent Raman and photoluminescence spectroscopy, where localized exciton states perpetuated at 78 K that are gaining increasing attention for single photon emitters for quantum information processing. The exciton and phonon dynamics in 2D WSe2 were further analyzed to unveil other multi-body states besides localized excitons, such as trions whose population densities also evolved with temperature. The phonon lifetime, which is another interesting aspect of phonon dynamics, is calculated in 2D layered WSe2 using Raman spectroscopy for the first time and the influence of external stimuli such as temperature and laser power on the phonon behavior was also studied. Furthermore, we investigated the thermal properties in 2D WSe2 in a suspended architecture platform, and the thermal conductivity in suspended WSe2 was found to be ~ 1940 W/mK which was enhanced by ~ 4X when compared with substrate supported regions.
We also studied the use of halide-assisted low-pressure chemical vapor deposition (CVD) with NaCl to help to reduce the growth temperature to ∼750 °C, which is lower than the typical temperatures needed with conventional CVD for realizing 1L WSe2. The synthesis of monolayer WSe2 with high crystalline and optical quality using a halide assisted CVD method was successfully demonstrated where the role of substrate was deemed to play an important role to control the optical quality of the as-grown 2D WSe2. For example, the crystalline, optical and optoelectronics quality in CVD-grown monolayer WSe2 found to improve when sapphire was used as the substrate. Our work provides fundamental insights into the electronic, optoelectronic and quantum properties of WSe2 to pave the way for high-performance electronic, optoelectronic, and quantum-optoelectronic devices using scalable synthesis routes.
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Katukuri, Vamshi Mohan [Verfasser], den Brink Jeroen [Akademischer Betreuer] van, and Hermann [Akademischer Betreuer] Stoll. "Quantum chemical approach to spin-orbit excitations and magnetic interactions in iridium oxides / Vamshi Mohan Katukuri. Gutachter: Jeroen van den Brink ; Hermann Stoll. Betreuer: Jeroen van den Brink." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://d-nb.info/1069096342/34.
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Bull, James. "Application of Quantum Mechanics to Fundamental Interactions in Chemical Physics: Studies of Atom-Molecule and Ion-Molecule Interactions Under Single-Collision Conditions: Crossed Molecular Beams; Single-Crystal Mössbauer Spectroscopy: Microscopic Tensor Properties of ⁵⁷Fe Sites in Inorganic Ferrous High-Spin Compounds." Thesis, University of Canterbury. Department of Chemistry, 2010. http://hdl.handle.net/10092/4292.
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As part of this project and in preparation for future experimental studies of gas-phase ion-molecule reactions, extensive modification and characterization of the crossed molecular beam machine in the Department of Chemistry, University of Canterbury has been carried out. This instrument has been configured and some
preliminary testing completed to enable the future study of gas-phase ion-molecule collisions of H⁺₃ and Y⁻ (Y
= F, Cl, Br) with dipole-oriented CZ₃X (Z = H, F and X = F, Cl, Br). Theoretical calculations (ab initio
and density functional theory) are reported on previously experimentally characterized Na + CH₃NO₂, Na + CH₃NC, and K + CH₃NC systems, and several other systems of relevance. All gas-phase experimental and theoretical studies have the common theme of studying collision orientation dependence of reaction under singlecollision
conditions. Experimental measurements, theoretical simulations and calculations are also reported on some selected ferrous (Fe²⁺) high-spin (S=2) crystals, in an attempt to resolve microscopic contributions of two fundamental macroscopic tensor properties: the electric-field gradient (efg); and the mean square displacement (msd) in the case when more than one symmetry related site of low local point-group symmetry contributes to the same quadrupole doublet. These determinations have been made using the nuclear spectroscopic technique of Mössbauer spectroscopy, and complemented with X-ray crystallographic measurements.
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Leclerc, Arnaud. "Élaboration d’un propagateur global pour l’équation de Schrödinger & Application à la photodynamique." Thesis, Besançon, 2012. http://www.theses.fr/2012BESA2002/document.
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La Méthode de la Trajectoire Adiabatique Contrainte est développée dans le but de résoudre globalementl’équation de Schrödinger. Cette méthode utilise le formalisme de Floquet et une décomposition de Fourier pourdécrire les dépendances temporelles. Elle transforme ainsi un problème dynamique en un problème aux valeurspropres partiel dans un espace de Hilbert étendu au temps. Cette manipulation requiert l’application decontraintes sur les conditions initiales de l’état propre de Floquet recherché. Les contraintes sont appliquées parl’intermédiaire d’un opérateur absorbant artificiel. Cet algorithme est adapté à la description de systèmes dirigéspar des hamiltoniens dépendant explicitement du temps. Il ne souffre pas de l’accumulation d’erreurs au cours dutemps puisqu’il fournit une solution globale ; les erreurs éventuelles proviennent de la non-complétude des basesfinies utilisées pour la description moléculaire ou temporelle et de l’imperfection du potentiel absorbant dépendantdu temps nécessaire pour fixer les conditions initiales. Une forme générale de potentiel absorbant a étédéveloppée pour être en mesure d’intégrer un problème avec une condition initiale quelconque. Des argumentsrelatifs au suivi adiabatique dans le cas de Hamiltoniens non-hermitiens sont également présentés. Nous insistonssur le rôle des facteurs de phase géométrique. Les méthodes développées sont appliquées à des systèmesatomiques ou moléculaires soumis à des impulsions laser intenses, en relation avec la problématique du contrôlemoléculaire. Nous considérons plusieurs exemples : modèles d’atomes à deux ou trois niveaux, ion moléculairehydrogène et molécules froides de sodiumThe Constrained Adiabatic Trajectory Method (CATM) allows us to compute global solutions of the time-dependent Schrödinger equation using the Floquet formalism and Fourier decomposition. The dynamical problem is thustransformed into a “static” problem, in the sense that the time will be included in an extended Hilbert space. Thisapproach requires that suitable constraints are applied to the initial conditions for the relevant Floquet eigenstate.The CATM is well suited to the description of systems driven by Hamiltonians with explicit and complicated timevariations. This method does not have cumulative errors and the only error sources are the non-completeness ofthe finite molecular and temporal basis sets used, and the imperfection of the time-dependent absorbing potentialwhich is essential to impose the correct initial conditions. A general form is derived for the absorbing potential,which can reproduce any dispersed boundary conditions. Arguments on adiabatic tracking in the case of nonhermitianHamiltonians are also presented. We insist on the role of geometric phase factors. The methods areapplied to atomic and molecular systems illuminated by intense laser pulses, in connection with molecular controlproblems. We study several examples : two or three-level atomic models, hydrogen molecular ion, cold sodiummolecules
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Schahl, Adrien. "Interactions polysaccharides-lipides : étude théorique et expérimentale combinant calculs de dynamique moléculaire, calculs quantiques de spectres RMN 13C et RMN 13C à l'état solide." Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30178.
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Les interactions entre polysaccharides et lipides forment aujourd'hui un vaste domaine d'étude, présentant notamment un intérêt particulier pour les industries alimentaires et pharmaceutiques. Nous savons que l'amylose, un polysaccharide composé de résidus glucose branchés en [apha 1→4] essentiellement linéaire, peut encapsuler de petites molécules hydrophobes formant ce qu'on appelle un polymorphe V. L'étude de ce type de complexes pourrait permettre de développer de nouvelles voies de formulations de substances bioactives ou de nouveaux adjuvants de vaccins. Ce type d'interactions pourraient aussi être présentes dans d'autres systèmes biologiques, tels que dans la capsule de Mycobacterium tuberculosis. En effet, cette couche externe enveloppant le bacille contient majoritairement un polysaccharide ramifié analogue à l'amylose appelé alpha-glucane mais aussi de multiples lipides connus comme étant des facteurs de virulence de cette mycobactérie, tels que les dimycocérosates de phthiocérol ou les dimycolates de tréhalose. La mise en évidence et l'analyse de ce type d'interaction pourrait permettre de comprendre l'organisation de cette capsule et d'en savoir plus sur ses fonctions biologiques. Ce manuscrit présente une étude mêlant méthodes théoriques et expérimentales de caractérisation des interactions au sein de complexes d'amylose en présence de lipides "classiques" ou mycobactériens ainsi que de systèmes comprenant des polysaccharides ramifiés. La première partie de ce manuscrit présente deux études purement théoriques portant sur des complexes d'amylose en présence d'acide palmitique et de doubles hélices d'amylose appelées polymorphe B. En utilisant une méthodologie couplant dynamique moléculaire (MD) et calculs de paramètres RMN par DFT, nous avons pu caractériser le nombre minimum de résidus glucose nécessaires pour former de manière stable le polymorphe V autour de l'acide palmitique. Nous avons pu aussi démontrer l'impact de la longueur du polymère sur le calcul de paramètre RMN et qu'il était crucial d'introduire le caractère dynamique de ces polymorphes afin d'obtenir des résultats en accord avec l'expérience. Concernant le polymorphe B, nous avons pu montrer qu'il était nécessaire de prendre en compte les conditions périodiques du système afin de pouvoir différencier deux types de résidu au sein de la double hélice, comme cela est observé expérimentalement sur des échantillons cristallins.[...]Polysaccharide-lipid interactions now form a vast domain of study, of particular interest to the pharmaceutical and food industries. We already know that amylose, an essentially linear polysaccharide composed of [alpha 1→4]-linked glucose moieties, can form helices around small hydrophobic molecules and lipidic chains. These helical structures are called V polymorphs and their study may allow the development of new ways to deliver bioactive compounds, or of new vaccine adjuvants. This type of interaction might also be found in other biological systems, such as in the capsule of Mycobacterium tuberculosis. Indeed, this external layer covering the bacillus is composed mostly of a large branched polysaccharide analogous to amylose, called alpha-glucan, but it also contains numerous lipids, such as phtiocerol dimycocerosates or trehalose dimycolates, known to be virulence factors of the mycobacterium. Demonstration of the existence of such interactions and their study may lead to a better understanding of the capsule and its biological functions. This manuscript describes a study combining theoretical and experimental methods to characterize the interactions amongst amylose complexes formed in the presence of classical and mycobacterial lipids and in systems composed of branched polysaccharides. The first part of this work describes two purely theoretical studies on amylose complexed with palmitic acid and on amylose double helices called B polymorphs. Using molecular dynamics (MD) simulations and calculations of Nuclear Magnetic Resonance (NMR) parameters at the Density Functional Theory (DFT) level, we were able to define the minimum number of glucose residues needed to former a stable V polymorph around a palmitic acid molecule. We could also show that the number of residues has a direct impact on the calculation of NMR parameters and that it is crucial to consider the dynamic behavior of these polymers to obtain results that fit well to experimental data. Regarding the B polymorph, we showed that it is essential/necessary to consider the periodic conditions of the system to be able to characterize two different residue positions, as has been observed experimentally. To the best of our knowledge, no V polymorph has been characterized in the presence of lipids composed of several lipidic chains. The second part of this manuscript describes several such complexes, formed in the presence of classical and mycobacterial lipids composed of 1, 2 or 4 lipidic chains, and their analysis by solid-state NMR. We elaborated a model describing the different equilibria implicated in the complexation process and could demonstrate that the primary structure of the lipids was one of the key factors. [...]
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Yang, Hui. "Theoretical Studies of Molecular Recognition in Protein-Ligand and Protein-Protein Complexes." University of Toledo / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1282339026.
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Krishnamurty, M. S. "Quantum chemical studies on zeolite cluster models: electronic structure and interaction with small molecules." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 1999. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2949.
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Sergentu, Dumitru-Claudiu. "Géométries, electronic structures, and physico-chemical porperties of astatine species : an application of relativistic quantum mechanics." Thesis, Nantes, 2016. http://www.theses.fr/2016NANT4024/document.
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Les tentatives menées pour détruire des cellules cancéreuses avec les agents radiothérapeutiques à base de 211 At qui ont été synthétisés jusqu’à présent ne sont pas encore pleinement satisfaisantes car elles sont entachées par une deastatination in vivo. Étant donné que ce problème est lié aux connaissances actuelles qui sont limitées concernant la chimie de base de l’astate et de ses espèces, des recherches fondamentales combinant des expériences à l’échelle des ultra-traces et des études théoriques ont été lancées. Dans cette thèse, une étude théorique de plusieurs espèces de l’astate est réalisée au moyen de méthodes relativistes basées sur la théorie de la fonctionnelle de la densité ou des méthodes à basées sur la fonction d’onde. Tout d'abord, les méthodes qui peuvent être utilisées pour faire des prédictions pertinentes sont établies. A l’aide de ces approches, nous rationaliserons les structures électroniques, géométries et propriétés physicochimiques des différents systèmes d'intérêt théorique ou expérimental, en particulier les espèces AtF3 et AtO+. Finalement, nous identifierons formellement une nouvelle espèce de l’astate à l’aide de résultats expérimentaux et de calculs, ce qui non seulement complète le diagramme de Pourbaix de l’astate en milieu aqueux non complexant, mais aussi donne des informations cruciales pour identifier des conditions expérimentales pour rendre le plus « réactif » possible le précurseur At−, qui est de nos jours impliqué dans la synthèse d’agents radiothérapeutiques innovantsTrials to destroy cancer cells with currently synthesized 211 At-based radiotherapeutic agents are not yet fully satisfactorily since they resume to in vivo deastatination. Since this issue is related to the limited knowledge of the basic chemistry of At and its species, fundamental researches combining ultra-trace experiments and computational studies have been initiated. In this thesis, a computational study of several At species is performed, by means of relativistic density functional theory and wave-function-based calculations. First, the quantum mechanical approaches that can safely be used to make adequate predictions are established. Using these approaches, we attempt to rationalize the electronic structures, geometries, and physico-chemical properties of various systems of theoretical and/or experimental interest, in particular the AtF3 and AtO+ ones. By the end, we firmly identify a new At species by combining outcomes of experiments and calculations. This new species not only completes the Pourbaix diagram of At in aqueous and non-complexing media, but also gives clues of identifying experimental conditions to make best reactive the At– precursor, which is currently involved in the synthesis of promising radiotherapeutic agents
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Sulzer, David. "Modélisation des interactions faibles en théorie de la fonctionnelle de la densité." Phd thesis, Université de Strasbourg, 2012. http://tel.archives-ouvertes.fr/tel-00945896.
Full textAbstract:
Les descriptions des interactions faibles et notamment de la dispersion représentent un problème majeur pour la théorie de la fonctionnelle de la densité. En effet, le caractère fortement local des fonctionnelles rend problématique la description des interactions à longue-portée. Aussi, plusieurs stratégies sont envisagées: des corrections des fonctionnelles existantes ou une introduction de méthodes post-Hartree-Fock par séparation de portée. Des résultats dans les deux cas sont exposés. Tout d'abord, la méthodologie hybride est appliquée à des dimères de métaux de transition (Cr2, Mn2 et Zn2). Ensuite, le calcul de coefficients de corrections pour la dispersion dans un cadre relativiste est présenté. Enfin, les interactions faibles peuvent également résulter de l'interaction d'une molécule avec un champ magnétique. Dans ce cadre, une modélisation de la modification de la densité électronique dans les systèmes aromatiques sous l'influence d'un champ magnétique extérieur est présentée.
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Bhowmick, Somnath. "Theory on lower bound energy and quantum chemical study of the interaction between lithium clusters and fluorine/fluoride." Thesis, Aix-Marseille, 2015. http://www.theses.fr/2015AIXM4394.
Full textAbstract:
En chimie quantique, le principe variationnel est largement utilisé pour calculer la limite supérieure de l'énergie exacte d'un système atomique ou moléculaire. Des méthodes pour calculer la valeur limite inférieure de l'énergie existent mais sont bien moins connues. Une méthode précise pour calculer une telle limite inférieure permettrait de fournir une barre d'erreur théorique pour toute méthode de chimie quantique. Nous avons appliqué des méthodes de type variance pour calculer différentes énergies limites inférieures de l'atome d'hydrogène en utilisant des fonctions de base gaussiennes. L'énergie limite supérieure se trouve être toujours plus précise que ces différentes limites inférieures, i.e. plus proche de l'énergie exacte. L'importance de points singuliers sur l'évaluation de valeurs moyennes d'opérateurs quantiques a également été soulignée.Nous avons étudié les réactions d'adsorption d'un atome de fluor et d'un ion fluorure sur de petits agrégats de lithium Li$_n$ (n=2-15), à l'aide de méthodes de chimie quantique précises. Pour le plus petit système, nous avons montré que la formation de complexes stables Li$_2$F et Li$_2$F$^-$ se produit par un transfert d'électrons sans barrière et à longue portée, de Li$_2$ vers F pour le système neutre et l'inverse pour le système anionique. De telles réactions pourraient être rapides à très basse température. De plus, les complexes formés présentent des caractéristiques uniques de "longue liaison". Pour les systèmes plus gros Li$_n$F/Li$_n$F$^-$ ($n\geqslant4$), nous avons montré que les énergies d'adsorption peuvent être aussi grandes que 6~eV selon le site d'adsorption et que plus d'un état électronique est impliqué dans le processus d'adsorption. Les complexes formés présentent des propriétés intéressantes de "super alcalins" et pourraient servir d'unités de base dans la synthèse de composés à transfert de charge avec des propriétés ajustablesIn quantum chemistry, the variational principle is widely used to calculate an upper bound to the true energy of an atomic or molecular system. Methods for calculating the lower bound value to the energy exist but are much less known. An accurate method to calculate such a lower bound would allow to provide a theoretical error bar for any quantum chemistry method. We have applied variance-like methods to calculate different lower bound energies of a hydrogen atom using Gaussian basis functions. The upper bound energy is found to be always more accurate than the lower bound energies, i.e. closer to the exact energy. The importance of singular points on mean value evaluation of quantum operators has also been brought to attention.The adsorption reactions of atomic fluorine (F) and fluoride (F$^-$) on small lithium clusters Li$_n$ (n=2-15) have been investigated using accurate quantum chemistry ab initio methods. For the smallest system, we have shown that the formation of the stable Li$_2$F and Li$_2$F$^-$ complexes proceeds via a barrierless long-range electron transfer, from the Li$_2$ to F for the neutral and conversely from F$^-$ to Li$_2$ for the anionic system. Such reactions could be fast at very low temperature. Furthermore, the formed complexes show unique long bond characteristics. For the bigger Li$_n$F/Li$_n$F$^-$ systems ($n\geqslant 4$), we have shown that the adsorption energies can be as large as 6~eV depending on the adsorption site and that more than one electronic state is implied in the adsorption process. The formed complexes show interesting "superalkali" properties and could serve as building blocks in the synthesis of charge-transfer compounds with tunable properties
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Takacs, Zoltan. "Chloromethane Complexation by Cryptophanes : Host-Guest Chemistry Investigated by NMR and Quantum Chemical Calculations." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-81472.
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Host–guest complexes are widely investigated because of their importance in many industrial applications. The investigation of their physico–chemical properties helps understanding the inclusion phenomenon. The hosts investigated in this work are cryptophane molecules possessing a hydrophobic cavity. They can encapsulate small organic guests such as halo–methanes (CH2Cl2, CHCl3). The encapsulation process was investigated from both the guest and the host point of view. With the help of Nuclear Magnetic Resonance (NMR), the kinetics of complex formation was determined. The information was further used to obtain the activation energies of the processes. Having done this on five different cryptophanes, it is possible to relate the energies to structural differences between the hosts. Via the dipolar interaction between the guest’s and host’s protons, one can get information on the orientation of the guest inside the cavity. Moreover, the dynamics of the guest can be further investigated by its relaxation properties. This revealed restricted motion of the guest inside the host cavity. Not only the nature of the guest plays an important role. The host is also changing its properties upon encapsulation. All the cryptophanes investigated here can exchange rapidly between many conformers. These conformers have different–sized cavities. Quantum chemical optimization of the structure of the conformers makes volume estimation possible. Not only the cavity volumes, but also the quantum-chemically obtained energies and the calculated chemical shifts of the carbon–13 atoms can be helpful to follow the changes of the host upon complex formation. The host cannot be considered as a rigid entity. Analysis of variable temperature proton and carbon-13 spectra shows that the encapsulation can be considered as a mixture of conformational selection and induced fit. The structures of the formed complexes are further investigated by means of two-dimensional nuclear Overhauser spectroscopy (NOESY). The complex formation, its kinetics and thermodynamics are found to be a complicated function of structure elements of the host, the cavity size and the guest size and properties.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Accepted. Paper 5: Manuscript.
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Maxwell, Peter. "FFLUX : towards a force field based on interacting quantum atoms and kriging." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/fflux-towards-a-force-field-based-on-interacting-quantum-atoms-and-kriging(72a8462a-6907-4f3d-82da-4c182e5a644d).html.
Full textAbstract:
Force fields have been an integral part of computational chemistry for decades, providing invaluable insight and facilitating the better understanding of biomolecular system behaviour. Despite the many benefits of a force field, there continue to be deficiencies as a result of the classical architecture they are based upon. Some deficiencies, such as a point charge electrostatic description instead of a multipole moment description, have been addressed over time, permitted by the ever-increasing computational power available. However, whilst incorporating such significant improvements has improved force field accuracy, many still fail to describe several chemical effects including polarisation, non-covalent interactions and secondary/tertiary structural effects. Furthermore, force fields often fail to provide consistency when compared with other force fields. In other words, no force field is reliably performing more accurately than others, when applied to a variety of related problems. The work presented herein develops a next-generation force field entitled FFLUX, which features a novel architecture very different to any other force field. FFLUX is designed to capture the relationship between geometry and energy through a machine learning method known as kriging. Instead of a series of parameterised potentials, FFLUX uses a collection of atomic energy kriging models to make energy predictions. The energies describing atoms within FFLUX are obtained from the Interacting Quantum Atoms (IQA) energy partitioning approach, which in turn derives the energies from the electron density and nuclear charges of topological atoms described by Quantum Chemical Topology (QCT). IQA energies are shown to provide a unique insight into the relationship between geometry and energy, allowing the identification of explicit atoms and energies contributing towards torsional barriers within various systems. The IQA energies can be modelled to within 2.6% accuracy, as shown for a series of small systems including weakly bound complexes. The energies also allow an interpretation of how an atom feels its surrounding environment through intra-atomic, covalent and electrostatic energetic descriptions, which typically are seen to converge within a ~7 - 8 A horizon radius around an atom or small system. These energy convergence results are particularly relevant to tackling the transferability theme within force field development. Where energies are seen to converge, a proximity limit on the geometrical description needed for a transferable energy model is defined. Finally, the FFLUX force field is validated through successfully optimising distorted geometries of a series of small molecules, to near-ab initio accuracy.
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Norberg, Daniel. "Quantum Chemical Studies of Radical Cation Rearrangement, Radical Carbonylation, and Homolytic Substitution Reactions." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8178.
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Oksuz, Nevin. "Quantum-chemical Study Of Geometrical And Electronic Structures Of Aromatic Five-membered Heterocyclic Oligomers In The Ground And Lowest Singlet Excited States." Master's thesis, METU, 2004. http://etd.lib.metu.edu.tr/upload/12605397/index.pdf.
Full textAbstract:
The nature of the ground state and the first (lowest) singlet excited state geometrical conformations and electronic transitions in the aromatic five-membered heterocyclic oligomers &ndasholigothiophenes (nT), oligofurans (nF), and oligopyrroles (nP)- containing up to six monomer units (total of 18 molecules) were explored using several computational methodologies. Geometry optimizations were carried out at Austin Model 1 (AM1), Restricted Hartree-Fock (RHF/6-31G*), and Density Functional Theory (DFT, B3LYP/6-31G*) levels for the ground-state conformations of these structurally well-defined heterocyclic oligomers. The Configuration Interaction Singles (CIS) method with the 6-31G* basis set was chosen in computation of the optimal geometry of the lowest singlet excited state. Lowest singlet excitation S1ß
S0 energies were calculated using the Zerner&rsquo
s Intermediate Neglect of Differential Overlap for Spectroscopy (ZINDO/S), CIS (CIS/6-31G*), and Time-Dependent DFT (TDDFT/6-31G* and TDDFT/6-31+G*) methods. In computation of the emission S1à
S0 energies, we have employed all methods above except ZINDO/S. In investigation of geometries of the ground and lowest singlet excited state, we compared the bond length alternation (BLA) parameters, Dri in the conjugated backbone of the oligomers. Saturation of the geometrical parameters at the center of oligomers was observed after a certain chain length. Among all methodologies used in computation of excitation (S1ß
S0) and emission (S1à
S0) energies, TDDFT results showed the best agreement with experimental data. Fits of computed and experimental excitation energies to an exponential function using the least squares method enabled us to predict Effective Conjugation Length (ECL) values. We obtained the ECLs of 17 (17), 16 (15), and 14 (13) monomer units for polythiophene (PTh), polyfuran (PFu), and polypyrrole (PPr), which have very good agreement with the results obtained from the fits of experimental data (the values in parentheses).
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Luschtinetz, Regina. "Theoretical studies towards a ferroelectric organic field-effect transistor based on functional thiophene molecules." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-102735.
Full textAbstract:
Thin-film organic field effect transistors (OFETs) have attracted growing interest in recent years due to their promising electrical, optical and mechanical properties. Especially, oligothiophenes and their derivates are candidates with good prospects for application as the organic semiconducting material in such devices. They possess an extended, polarisable aromatic π-electron system that promotes a high structural arrangement of the molecules. The charge transport in the organic film is realised in the direction perpendicular to the plane of the thiophene rings via a hopping transport mechanism. Thus, a good π-π-overlap and a consequent stacking of the thiophene molecules in the film perpendicular to the gate substrate is essential to achieve excellent electric properties such as high charge carrier mobilities and low resistive losses.
The highly polarisable thiophene-based molecules are also very attractive materials that are potentially applicable as the field-sensitive organic semiconducting component of a ferroelectric OFET device. In such a device, the dielectric gate element of a conventional OFET setup is substituted by a ferroelectric substrate. The electric field that is induced by the polarisation of the ferroelectric material serves as gate field and controlls the charge injection and charge density inside the device.
In this thesis, thiophene-based molecules are investigated in detail with respect to their application as field-sensitive organic semiconducting component in a ferroelectric OFET device employing quantum-chemical ab initio and DFT-based methods. We demonstrate that the phosphonic acids can bind the organic molecules to the dielectric or ferroelectric material and well-anchored, robust self-assembled monolayers are formed. Furthermore, special focus is put on the influence of the intermolecular interactions among the organic molecules on the technologically relevant structural and electronic properties. It is found that the CN···HC hydrogen bond link the molecules into extended ribbons, but the π-π-stacking-stacking interaction is the main driving force in the self-assembly of the molecules. We also establish in detail the influence of the electric field on the phosphonic acid anchoring molecule and some quarterthiophene derivates.
For the latter, the strongest field-sensitivity is obtained for an external electric field aligned parallel to the extension of the thiophene framework. Hence, they are suitable to act as the field-sensitive organic components in devices that take advantage of a band-gap engineering. Moreover, the present results emphasise the importance of the adsorption morphology of the molecules in the film in a π-stacked fashion with their longitudinal axis oriented parallel to the (orthonormal) electric field induced by the ferroelectric substrate.
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Weil, Thierry. "Etude theorique du transport perpendiculaire aux couches dans les semiconducteurs 3-5 modules suivant une dimension." Paris 6, 1987. http://www.theses.fr/1987PA066099.
Full textAbstract:
Proposition d'un modele pour le transport inelastique et application au transport assiste par phonons entre deux puits quantiques, a la capture des porteurs par le puits quantique d'un laser sch, au transport dans les pseudoalliages quaternaires et dans les superreseaux. Analyse des differents modeles de l'effet tunnel et discussion de la duree de l'effet tunnel; application aux diodes a double barriere et mise en evidence de l'equivalence des descriptions basees sur l'effet tunnel resonnant et sur l'effet tunnel sequentiel, au moins en regime continu; effets des diffusions, developpement d'un modele sequentiel a partir du formalisme d'oppenheimer. Algorithme de calcul du transport perpendiculaire dans les heterostructures (approche de la cao des structures de bande)
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Katukuri, Vamshi Mohan. "Quantum chemical approach to spin-orbit excitations and magnetic interactions in iridium oxides." Doctoral thesis, 2014. https://tud.qucosa.de/id/qucosa%3A28539.
Full textAbstract:
In the recent years, interest in TM oxides with 5d valence electrons has grown immensely due to the realization of novel spin-orbit coupled ground states. In these compounds, e.g., iridates and osmates, the intriguing situation arises where the spin-orbit and electron-electron interactions meet on the same energy scale. This has created a new window of interest in these compounds since the interplay of crystal field effects, local multiplet physics, spin-orbit couplings, and intersite hopping can offer novel types of correlated ground states and excitations. In 5d5 iridates, a spin-orbit entangled j = 1/2 Mott insulating state has been realized recently. A remarkable feature of such a ground state is that it gives rise to anisotropic magnetic interactions. The 2D honeycomb-lattice 213 iridium oxides, A2IrO3 (A=Li,Na), have been put forward to host highly anisotropic bond-dependent spin-spin interactions that resemble the Kitaev spin model, which supports various types of topological phases relevant in quantum computing. The 2D square-lattice 214 iridates Sr2IrO4 and Ba2IrO4 are, on the other hand, appealing because of their perceived structural and magnetic simi- larity to La2CuO4, the mother compound of the cuprate high-Tc superconductors. This has promoted the latter iridium oxide compounds as novel platforms for the search of high-Tc superconductivity.
To put such considerations on a firm footing, it is essential to quantify the different coupling strengths and energy scales, as they for instance appear in effective Hamiltonian descriptions of these correlated systems. Moreover, it is important to correctly describe their effects. In this thesis, the electronic structure and magnetic properties of 5d5 (mainly 214 and 213) iridates are studied using wave-function-based quantum chemistry methods. These methods are fully ab initio and are capable of accurately treating the electron-electron interactions without using any ad hoc parameters. The spin-orbit entangled j = 1/2 ground state in 214, 213 and other lower symmetry Sr3CuIrO6 and Na4Ir3O8 iridates is first analyzed in detail, by studying the local electronic structure of the 5d5 Ir4+ ion. We establish that the longer-range crystal anisotropy, i.e., low-symmetry fields related to ionic sites beyond the nearest neighbor oxygen cage, strongly influence the energies of Ir d levels. The ground state in all the compounds studied is j = 1/2 like with admixture from j ≃ 3/2 states ranging from 1 – 15 %. Further, the average j ≃ 1/2 → j ≃ 3/2 excitation energy we find is around 0.6 eV.
The NN magnetic exchange interactions we computed for 214 iridates are predominantly isotropic Heisenberg-like with J ~ 60 meV, 3 – 4 times smaller than found in isostructural copper oxides. However, the anisotropic interactions are an order of magnitude larger than those in cuprates. Our estimates are in excellent agreement with those extracted from experiments, e.g., resonant inelastic x-ray scattering measurements. For the 213 honeycomb-lattice Na2IrO3 our calculations show that the relevant spin Hamiltonian contains further anisotropic terms beyond the Kitaev-Heisenberg model. Nevertheless, we predict that the largest energy scale is the Kitaev interaction, 10 to 20 meV, while the Heisenberg superexchange and off-diagonal symmetric anisotropic couplings are significantly weaker. In the sister compound Li2IrO3, we find that the structural inequivalence between the two types of Ir-Ir links has a striking influence on the effective spin Hamiltonian, leading in particular to two very different NN superexchange pathways, one weakly AF (~ 1 meV) and another strongly FM (−19 meV). The latter gives rise to rigid spin-1 triplets on a triangular lattice.
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Shukla, A., E. Khan, K. Srivastava, K. Sinha, P. Tandon, and Venu R. Vangala. "Study of hydrogen bonding interactions and chemical reactivity analysis of nitrofurantoin–3-aminobenzoic acid cocrystal using quantum chemical and spectroscopic (IR, Raman, 13C SS-NMR) approaches." 2017. http://hdl.handle.net/10454/12402.
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YesInvestigations of structural reactivity, molecular interactions and vibrational characterization of pharmaceutical drugs are helpful in understanding their behaviour. The aim of this study is to determine the molecular, electronic and chemical properties of the antibiotic drug nitrofurantoin (NF), after cocrystallisation with 3-aminobenzoic acid (3ABA) and to understand how those changes lead to variation of properties in the cocrystal NF–3ABA. NF–3ABA formation is explained by stabilization via the hydrogen-bond network between NF and 3ABA molecules. It is thoroughly characterized by IR, Raman and CP-MAS solid-state 13C NMR techniques, along with quantum chemical calculations. The results of IR, Raman, and 13C NMR analyses showed that imide N–H23 and C12[double bond, length as m-dash]O of NF interact with the acid C[double bond, length as m-dash]O and –OH groups in 3-ABA, respectively. Therefore the IR, Raman, and 13C NMR spectra verified the formation of N–H⋯O and O–H⋯O hydrogen bonds. To study hydrogen bonding interactions theoretically in NF–3ABA, two functionals B3LYP and wB97X-D have been used. A comparison is made between the results obtained by B3LYP and those predicted at the wB97X-D level. It is found that wB97X-D is best applied density functional theory (DFT) functional to describe the hydrogen bonding interactions. The strength and nature of hydrogen bonding in NF–3ABA have been analysed by quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. To validate the results obtained by QTAIM theory and to study the long-range forces, such as van der Waals interactions, the steric effects in NF–3ABA, the reduced density gradient (RDG) and the isosurface have been plotted using Multiwfn software. QTAIM and isosurface analysis suggested that the hydrogen bonding interactions present in NF–3ABA are moderate in nature. The calculated HOMO–LUMO energy gap shows that NF–3ABA is more active than NF and 3ABA. Chemical reactivity descriptors are calculated to understand the various aspects of pharmacological sciences. Chemical reactivity parameters show that NF–3ABA is softer and chemically more reactive than NF. The results suggest that cocrystals can be a feasible alternative for positively changing the targeted physicochemical properties of an active pharmaceutical ingredient (API).
V. R. Vangala acknowledges the financial support of the Royal Society of Chemistry for mobility grant (2015/17).
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Shukla, A., E. Khan, K. Srivastava, K. Sinha, P. Tandon, and Venu R. Vangala. "Study of molecular interactions and chemical reactivity of the nitrofurantoin-3-aminobenzoic acid cocrystal using quantum chemical and spectroscopic (IR, Raman,13C SS-NMR) approaches." 2017. http://hdl.handle.net/10454/17779.
Full textAbstract:
NoInvestigations of structural reactivity, molecular interactions and vibrational characterization of pharmaceutical drugs are helpful in understanding their behaviour. The aim of this study is to determine the molecular, electronic and chemical properties of the antibiotic drug nitrofurantoin (NF), after cocrystallisation with 3-aminobenzoic acid (3ABA) and to understand how those changes lead to variation of properties in the cocrystal NF–3ABA. NF–3ABA formation is explained by stabilization via the hydrogen-bond network between NF and 3ABA molecules. It is thoroughly characterized by IR, Raman and CP-MAS solid-state 13C NMR techniques, along with quantum chemical calculations. The results of IR, Raman, and 13C NMR analyses showed that imide N–H23 and C12[double bond, length as m-dash]O of NF interact with the acid C[double bond, length as m-dash]O and –OH groups in 3-ABA, respectively. Therefore the IR, Raman, and 13C NMR spectra verified the formation of N–H⋯O and O–H⋯O hydrogen bonds. To study hydrogen bonding interactions theoretically in NF–3ABA, two functionals B3LYP and wB97X-D have been used. A comparison is made between the results obtained by B3LYP and those predicted at the wB97X-D level. It is found that wB97X-D is best applied density functional theory (DFT) functional to describe the hydrogen bonding interactions. The strength and nature of hydrogen bonding in NF–3ABA have been analysed by quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. To validate the results obtained by QTAIM theory and to study the long-range forces, such as van der Waals interactions, the steric effects in NF–3ABA, the reduced density gradient (RDG) and the isosurface have been plotted using Multiwfn software. QTAIM and isosurface analysis suggested that the hydrogen bonding interactions present in NF–3ABA are moderate in nature. The calculated HOMO–LUMO energy gap shows that NF–3ABA is more active than NF and 3ABA. Chemical reactivity descriptors are calculated to understand the various aspects of pharmacological sciences. Chemical reactivity parameters show that NF–3ABA is softer and chemically more reactive than NF. The results suggest that cocrystals can be a feasible alternative for positively changing the targeted physicochemical properties of an active pharmaceutical ingredient (API).
Royal Society of Chemistry for the mobility grant (2015/17); DST (New Delhi) under the DST purse programme; UGC under the BSR meritorious fellowship scheme; DST, India under the Indo-Brazil project
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Silva, W. Susil J. "Quantum chemical studies of adsorbate-surface interactions : application of cluster models to Al on graphite, slab models to H on Be(0001) and development of a novel embedded cluster models." Thesis, 1992. http://hdl.handle.net/10125/9509.
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Binder, Tobias. "Refining the chemical and kinetic decoupling description of thermally produced dark matter." Doctoral thesis, 2019. http://hdl.handle.net/11858/00-1735-0000-002E-E5E9-2.
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Višňák, Jakub. "Kvantově chemické algoritmy pro kvantové počítače." Master's thesis, 2012. http://www.nusl.cz/ntk/nusl-310395.
Full textAbstract:
Title: Quantum computing algorithms for quantum chemistry Author: Jakub Višňák Abstract: The topic of this study is the simulation of the quantum algorithm for the diagonalization of the matrix representation of the all-electron Dirac-Coulomb hamiltonian of the SbH molecule. Two different limited CI expansions were used to describe both the ground state (X 0+ ) and the first excited doublet (A 1) by simulating the Iterative Phase Estinamtion Algorith (IPEA). In the simulations numerically performed in this work, the "compact mapping" has been employed for the representation of the evolution operator exp(i Hˆ t); in the theoretical part of the work, the "direct mapping" is described as well. The influence of the metodics for choosing the initial eigenvector estimate is studied in both IPEA A and IPEA B variants. For those variants, the success probabilities pm are computed for different single-points on the SbH dissociation curves. The initial eigenvector estimates based on the "CISD(2)" method are found to be sufficient for both studied LCI-expansions up to internuclear distance R 6 a0. The pm dependence on the overlap between the eigenvector in question and its inital estimate - 2 0 is studied the for IPEA B method. The usability of the both variants of the IPEA in possible later calculations is...
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Luschtinetz, Regina. "Theoretical studies towards a ferroelectric organic field-effect transistor based on functional thiophene molecules." Doctoral thesis, 2012. https://tud.qucosa.de/id/qucosa%3A26383.
Full textAbstract:
Thin-film organic field effect transistors (OFETs) have attracted growing interest in recent years due to their promising electrical, optical and mechanical properties. Especially, oligothiophenes and their derivates are candidates with good prospects for application as the organic semiconducting material in such devices. They possess an extended, polarisable aromatic π-electron system that promotes a high structural arrangement of the molecules. The charge transport in the organic film is realised in the direction perpendicular to the plane of the thiophene rings via a hopping transport mechanism. Thus, a good π-π-overlap and a consequent stacking of the thiophene molecules in the film perpendicular to the gate substrate is essential to achieve excellent electric properties such as high charge carrier mobilities and low resistive losses.
The highly polarisable thiophene-based molecules are also very attractive materials that are potentially applicable as the field-sensitive organic semiconducting component of a ferroelectric OFET device. In such a device, the dielectric gate element of a conventional OFET setup is substituted by a ferroelectric substrate. The electric field that is induced by the polarisation of the ferroelectric material serves as gate field and controlls the charge injection and charge density inside the device.
In this thesis, thiophene-based molecules are investigated in detail with respect to their application as field-sensitive organic semiconducting component in a ferroelectric OFET device employing quantum-chemical ab initio and DFT-based methods. We demonstrate that the phosphonic acids can bind the organic molecules to the dielectric or ferroelectric material and well-anchored, robust self-assembled monolayers are formed. Furthermore, special focus is put on the influence of the intermolecular interactions among the organic molecules on the technologically relevant structural and electronic properties. It is found that the CN···HC hydrogen bond link the molecules into extended ribbons, but the π-π-stacking-stacking interaction is the main driving force in the self-assembly of the molecules. We also establish in detail the influence of the electric field on the phosphonic acid anchoring molecule and some quarterthiophene derivates.
For the latter, the strongest field-sensitivity is obtained for an external electric field aligned parallel to the extension of the thiophene framework. Hence, they are suitable to act as the field-sensitive organic components in devices that take advantage of a band-gap engineering. Moreover, the present results emphasise the importance of the adsorption morphology of the molecules in the film in a π-stacked fashion with their longitudinal axis oriented parallel to the (orthonormal) electric field induced by the ferroelectric substrate.