Dissertations / Theses on the topic 'Covalent approaches'
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Comí, Bonachí Marc. "Biobased polyurethanes with tunable properties through covalent and non-covalent approaches." Doctoral thesis, Universitat Rovira i Virgili, 2017. http://hdl.handle.net/10803/454764.
Full textEsta tesis está dirigida específicamente al desarrollo de poliuretanos (PU)s funcionalizados en la cadena lateral (FPU)s, sintetizados a partir de dioles funcionales que provienen de ácidos grasos y dos diisocianats diferentes; el diisocianato de isoforona (IPDI) y el diisocianato de hexametileno (HDI). Estos nuevos FPUs presentan una amina terciaria y grupos alquilo, alilo, propargilo o la combinación de éstos en posiciones de cadena lateral. Posteriormente los FPUs se modifican mediante dos mecanismos de post-polimerización basados en enlaces covalentes o en enlaces no covalentes.En el primer caso, se llevan a cabo una serie de reacciones fotoiniciadas de acoplamiento tiol-eno/ino entre el grupo alilo y propargilo que presentan los FPUs (formados a partir de IPDI), y tioglicerol. Los hidroxi-PUs obtenidos, exhiben una mejora de su carácter hidrófilo. Alternativamente, los FPUs que contienen sólo una amina terciaria como grupo funcional situado en la cadena lateral del PU, se mezclan con diferentes ácidos carboxílicos mediante una reacción de ácido base. Los PUs supramoleculares resultantes (SPU)s se caracterizan por espectroscopia para verificar la presencia de enlaces iónicos de hidrógeno que unen las cadenas de PU formando interacciones físicas. Además, se demuestra la correlación existente entre la estructura química y las propiedades térmicas y mecánicas de los materiales sintetizados. Estos materiales presentan prometedoras propiedades adaptativas. Por ejemplo, resaltan las buenas propiedades de regeneración y reciclaje/remodelación, debidas al carácter reversible de las interacciones físicas. Adicionalmente, estos elastómeros poseen una inherente capacidad de autorautorreparación, que en términos prácticos se podría ver como una mejora de su sostenibilidad. Finalmente, se sintetizan redes de PU que tienen un doble carácter estructural mediante enlaces iónicos de hidrógeno dinámicos y entrecruzamientos covalentes. La variación de la densidad de entrecruzamiento covalente introducido para cada una de estas redes produce un ajuste sistemático de las propiedades mecánicas y la sensibilidad del material al calor. Esta preparación demuestra una vía simple y eficaz para la fabricación de poliuretanos multifuncionales.
This Thesis is addressed to the development of side-chain functionalized polyurethanes (FPU)s, with enhanced properties, made from fatty acid-based functional diols and two different diisocyanates; isophorone diisocyanate (IPDI) and hexamethylene diisocyanate (HDI). The novel FPUs present tertiary amine and alkyl, allyl, propargyl moieties or the combination of these, as side-chain positions groups. The FPUs were further modified via two post-polymerization mechanisms based on covalent or non-covalent bonds. In the first case, photoinitiated thiol-ene/yne coupling reaction between allyl, propargyl-functionalized PUs (based on IPDI) and thioglycerol was carried out. Obtained hydroxyl-PUs exhibit different thermal and mechanical properties in comparison with precursor PUs. Moreover, the incorporation of hydroxyl groups leads to PUs with enhanced hydrophilicity. Alternatively, the FPU (based on IPDI) containing only tertiary amine pendant group was mixed with different carboxylic acids in an acid-base reaction. Supramolecular ionic PUs were characterized by spectroscopic tools to verify the presence of ionic hydrogen bond as ionic interaction. Correlation between structure and thermal and mechanical properties was demonstrated. Samples show rapid thermal reversibility and recyclability thanks to the reversible bonds. In addition, elastomeric supramolecular PUs networks were prepared from HDI and aminodiol. The resulting materials exhibit some promising adaptive material properties such as effective energy dissipation upon deformation through unzipping the ionic hydrogen bonding network, combined with good shape-regeneration property and recycling/reshaping capability arising from their recoverable nature. More importantly, the resulting biobased elastomers possess the inherent self-healing ability, which can be seen as an upgrade of their sustainability.A novel thermo-reversible network is constructed by the thiol-ene functionalized polyurethane via dynamic ionic hydrogen bonds and covalent cross-links. By varying the covalent cross-linking density, the mechanical properties and the stimuli-responsive behaviour can be systematically tuned. This synthesis demonstrates a simple and effective pathway to fabricate multifunctional polyurethanes with desired functions.
Gläske, Mareen [Verfasser]. "Tailoring the Optoelectronic Properties of Carbon Nanotubes : A Comparative Study of Covalent and Non-Covalent Functionalization Approaches / Mareen Gläske." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1185485910/34.
Full textMartínez, Carrión Alicia. "The Hydroformylation Reaction: from Covalent to Supramolecular Approaches and Operando Kinetic Studies." Doctoral thesis, Universitat Rovira i Virgili, 2020. http://hdl.handle.net/10803/669292.
Full textSe ha descrito la hidroformilación de alenos 1,1΄-disustitutidos catalizada por rodio empleando ligandos de tipo bisfosfito con un centro de regulación alejado del centro catalítico. El uso de sales de BArF de metales alcalinos como agentes de regulación aumentó la formación de aldehídos β,γ-insaturados (hasta un 60%), demostrando el principio de regulación supramolecular del sistema catalítico. La hidroformilación de octenos terminales e internos catalizada con cobalto y en presencia de Xantphos como ligando ha dado lugar a una alta selectividad en la formación de aldehídos. El control de la regioselectividad mediante la temperatura de la reacción y la proporción constante entre los diferentes regioisómeros de los aldehídos nos ha llevado a postular un proceso tándem de isomerización-hidroformilación bajo las condiciones optimizadas de reacción. Además, se ha llevado a cabo la hidroformilación de una mezcla de octenos, obteniéndose los aldehídos con alta selectividad y baja incidencia de reacciones secundarias, lo que la hace una ruta plausible a escala industrial. Además, el uso de ligandos regulados supramolecularmente con un centro de regulación alejado del centro catalítico permitió la hidroformilación enantioselectiva de aril vinil éteres, con una gran actividad catalítica, regioselectividad y ratio enantiomérico (hasta un 88% conversión, >99:1 b/l ratio, 97:3 er). Estudios de complejación revelaron la formación de especies catalíticas inactivas y la variación en la distribución de las especies catalíticamente activas en función del agente de regulación usado. Finalmente se realizaron estudios cinéticos sobre la reacción de hidroformilación enantioselectiva del acetato de vinilo empleando ligandos bisfosfito regulados mediante interacciones supramoleculares. El uso del Análisis de Normalización de Tiempo Variable permitió establecer el paso limitante de la reacción, situándolo en el comienzo del ciclo catalítico y ha permitido la obtención de los perfiles de reacción en ausencia de los periodos de inducción de formación el catalizador observados durante la reacción.
The rhodium-catalyzed hydroformylation of 1,1΄-disubstituted allenes was described employing bisphosphite ligands with a distal regulation site. The use of alkali metal BArF salts as regulation agents enhanced the formation of β,γ-unsaturated aldehydes (up to a 60% increase), proving the supramolecular regulation principle of the catalytic system. Cobalt-catalyzed hydroformylation of terminal and internal octenes in presence of Xantphos as ligand have displayed a high selectivity towards the formation of aldehydes. The control of the regioselectivity by the reaction temperature and the constant ratio in the different regioisomers led us to hypothesize that a tandem isomerization-hydroformylation transformation was taking place under optimized conditions. Furthermore, the hydroformylation of a mixture of octene isomers was reported with excellent aldehyde selectivity and diminished formation of side-products. Overall, the methodology may be suitable for industrial application. Moreover, the use of supramolecularly regulated ligands with distal regulation site enabled the rhodium-catalyzed enantioselective hydroformylation of aryl vinyl ethers, with high catalytic activity, regioselectivity and enantiomeric ratio (up to 88% conv, >99:1 b/l ratio and 97:3 er). Complexation studies revealed the formation of inactive catalytic species and a variation in the distribution of catalytic species based on the regulation agent used. Finally, kinetic studies of the rhodium-catalyzed enantioselective hydroformylation of vinyl acetate with a supramolecularly regulated bisphosphite complex were performed. The use of Variable Time Normalization Analysis allowed for the elucidation of the rate-determining step early in the catalytic cycle. Real kinetic profiles in the absence of catalyst induction periods observed during the reaction were also obtained.
Singh, Devanshi. "Non-covalent and macromolecular approaches to study protein binding, drug delivery and artificial blood." Thesis, University of Sheffield, 2018. http://etheses.whiterose.ac.uk/22376/.
Full textSquillaci, Bianca. "Approaches to the detection of adducts formed via the covalent binding of reactive metabolites to proteins." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/approaches-to-the-detection-of-adducts-formed-via-the-covalent-binding-of-reactive-metabolites-to-proteins(3b4ccc97-ea77-40d1-bb2b-2c4e70a1424d).html.
Full textMilovanovic, Milan. "Experimental and theoretical approaches coupled with thermochemistry of reactions in solution and the role of non-covalent interactions." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAF049.
Full textThis manuscript adressed several important chemical interactions/reactions taking place in solutuon by using Isothermal Titration Calorimetry (ITC) and static Density Functional Theory (DFT). Namely, this thesis dealt with: association of (frustrated) Lewis pairs ((F)LPs), cis-migration of methyl group within pentamethylmanganese induced by phosphines, aminolysis of Fischer carbenes, insertion of alkynes into palladacycles, affinity of various Lewis donors to hexafluoroisopropanol. The ITC proved to be powerful experimental technique for obteining reliable thermochemical data of sutudied systems. The static DFT-D calculations showed capability for proper estiamtion of thermodynamic reaction parameters when an influence of solvation is not sighnificant. Otherwise, when the influence of solvent is not innocent, the calculations moslty failed to reproduce the experimantal results. In addition, Both the experimantal and therortical results revield existance of larger molecular clusters in solution of FLPs emphasising a role of non-covalent interactions
Elkerdawy, Ahmed [Verfasser], and Tim [Akademischer Betreuer] Clark. "CADD Optimization by Using Quantum-Mechanical Approaches for a More Accurate Description of Non-Covalent Intermolecular Interactions / Ahmed Elkerdawy. Gutachter: Tim Clark." Erlangen : Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2013. http://d-nb.info/1054164487/34.
Full textGuo, Jingshu. "Structural Analysis of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches." University of Toledo / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1373036513.
Full textCreasey, Kate M. "Investigating the roles of arabidopsis polycomb-group genes in regulating flowering time and during plant development by (I) challenging silencing and (II) developing approaches to dissect Pc-G action." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/4025.
Full textLiebenberg, Liesl Eileen. "Non-covalent immobilisation of a ligand system : a new approach to affinity separation." Thesis, Stellenbosch : Stellenbosch University, 2003. http://hdl.handle.net/10019.1/53522.
Full textENGLISH ABSTRACT: Advances in pharmacology, biochemistry and biotechnology are increasingly dependant upon affinity chromatography as a preferred separation technique for the purification and characterisation of specific biomolecules. In the past few years avidin-biotin technology has been widely and successfully used in the fields of medicine, pharmacy, biology and biochemistry. The avidin-biotin complex (ABC) has been used as a mediator for affinity chromatography, affinity cytochemistry, immunoassay, histopathology, bioaffinity sensors, erosslinking and immobilisation studies. The main reason for the popularity of the ABC and its growing usefulness in biotechnology is the exceptionally high affinity (1015 M-l) and stability of the noncovalent interaction between avidin and biotin. The use of the ABC is broadening as different biotin derivatives and avidin-containing conjugates are becoming commercially available. The aim of this work was to evaluate the usefulness of a plutonic" FI 08 and the ABC conjugate to effect affinity separation. Towards this aim, the adsorption of plutonic" F108 onto hydrophobic polysulphone membrane surfaces was studied. This information was used to determine the theoretical maximum amount of pluronic" FI08 that will adsorb onto a unit surface area of the membrane. It is known that the polypropylene oxide (PPO) centre block ofthe pluronic" F I08 surfactant molecule governs the concentration of pluronic" F I 08 molecules that will adsorb onto a given hydrophobic surface. If the maximum coating concentration of plutonic" FI08 is known, one can assume that the maximum coating concentration of any pluronic derivative, with the same PPO centre block size, will be the same. Adsorption studies were carried out, the Langmuir adsorption isotherm was determined, and subsequently the fractional coating was calculated. The end-groups of plutonic" FI08 were modified as follows and the substituted pluronic was adsorbed onto a membrane that was to act as the solid support matrix in the development of an affinity system: Amino pluronic was synthesised by first tosylating pluronic" FI08, followed by azidation with NaN3 then reduction with LiAI~. The synthesised amino pluronic was then biotinylated using N-hydroxysuccinimide biotin ester. The suitability of this synthetic route was first assessed on a model compound, 2-methoxyethylamine, and validated by NMR (Nuclear Magnetic Resonance) spectroscopy. The synthetic protocol was then used to derivatise the larger pluronic molecule. The affinity system was tested on two different hydrophobic surfaces: polystyrene and polysulphone membranes (PSMs). Avidin-conjugated horseradish peroxidase was obtained and used to interact with the immobilised biotin. The enzymatic reaction of the coupled peroxidase converted the substrate, 2, 2'-azino-di-(3-ethyl-benzthiazoline-6-sulphonic acid) (ABTS) to a coloured product. The colour developed is proportional to the amount of biotin that was immobilised on the hydrophobic surfaces studied. Non-covalent immobilisation of the synthesised biotin-pluronic molecule was successfully obtained onto the hydrophobic polystyrene as well as the polysulphone membrane surfaces.
AFRIKAANSE OPSOMMING: Vooruitgang in die farmakologie, biochemie en biotegnologie word al meer afhanklik van affiniteits chromatografie as die verkose tegniek vir die suiwering en karaterisering van spesifieke biomolekules. Oor die afgelope jare het die avidien-biotien tegnologie homself as baie bruikbaar bewys in die mediese, farmakologiese, biologiese en biochemiese velde. Toepassings waar die avidien-biotien kompleks betrokke was sluit in die toepassing as 'n mediator vir affiniteits chromatografie, affiniteits sitologie, immuno bepalings, histopatologie, bioaffiniteits sensors sowel as kruisbinding en immobiliserings studies en vele meer. Die hoofrede vir die gewildheid van die avidien-biotien kompleks en die groeiende bruikbaarheid in die biotegnologie is die buitengewone hoë affiniteit (l015 M-I ) en stabiliteit van die nie-kovalente interaksie tussen avidien en biotien. Die toepassingsveld van die avidien-biotien kompleks word wyer met die verskeidenheid biotien derivate en avidien-bevattende konjugate wat kommersiëel beskikbaar is. Die doel van die werk wat hier gedokumenteer word is om die bruikbaarheid van Plutonic" FI08 en die avidien-biotien kompleks, vir gebruik in 'n affiniteits chromatografie sisteem, te evalueer. Om hierdie doel te bereik is die adsorpsie van Pluronic" FI08 aan hidrofobiese polisulfoon membraan oppervlaktes bestudeer. Die eksperimentele data wat gegenireer is, is gebruik om die teoretiese maksimum hoeveelheid Pluronic wat per eenheids oppervlakte membraan adsorbeer te bepaal. Dit is reeds bekend dat die polipropileen (PPO) middel blok van die Pluronic emulgant die konsentrasie van die geadsorbeerde Pluronic molekules op 'n gegewe hidrofobiese oppervlakte bepaal. Indien die maksimum bedekkingskonsentrasie VIr maksimum oppervlakbedekking van Plutonic" FI08 bekend is, kan teoreties aanvaar word dat die bedekkingskonsentrasie vir enige Pluronic derivaat met dieselfde grootte PPO blok dieselfde sal wees. Adsorpsiestudies was uitgevoer om die Langmuir adsorpsie isoterm te bepaal. Daaropvolgend was die fraksionele bedekking bereken. Amino-pluronic was gesintetiseer deur die eindpunte van Pluronic te derivatiseer. Hierdie Pluronic derivaat was gevolglik geadsorbeer aan 'n membraan wat gedien het as die soliede oppervlakte vir die ontwikkeling van 'n affiniteits chromatografie sisteem. Amino-pluronic was gesintetiseer deur Pluronic eers te tosileer en daarna te asideer met NaN3 en laastens te reduseer met LiAI~. Die produk was gebiotinileer deur gebruik te maak van N-hidroksisuksinimied-biotien-ester. Die bruikbaarheid van hierdie sintetiese roete is eers bepaal deur van 'n model verbinding, 2-metoksiëtielamien, gebruik te maak en dit met behulp van KMR (Kern Magnetiese Resonans) spektroskopie te karakteriseer. Die affiniteits sisteem is getoets op twee verskillende hidrofobiese oppervlaktes naamlik polistireen en polisulfoon membraan oppervlaktes. Avidien gekonjugeerd met 'n peroksiedase ensiem is gebruik om met die geïmmobiliseerde biotien te assosieer. Die ensiematiese reaksie van die gekoppelde peroksiedase het die substraat 2, 2' -azino-di-(3-etiel-benzthiazolien-6-sulfoonsuur) (ABTS) omgesit na 'n gekleurde produk, waar dit teenwoordig is. 'n Reeks wasstappe is gebruik om die gemodifiseerde peroksidase ensiem wat nie aan die hidrofobiese oppervlakte gekoppel nie, weg te spoel. Hierdeur is die mate van binding aan die hirofobiese oppervlakte gekwantifiseer deur die kleur te kwantifiseer wat ontwikkelomdat die kleurontwikkeling direk proporsioneel is aan die hoeveelheid peroksidase wat nog aan die membraan gekoppel is. Nie-kovalente immobilisasie van die gesintetiseerde biotien-pluronic molekule is suksesvolop beide die hidrofobiese polistireen oppervlakte sowel as die polisulfoon membraan verkry.
della, Sala Flavio. "Hydrazone exchange in nanoparticle monolayers : a dynamic covalent approach for controlling nanomaterial properties." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/6766.
Full textBeneteau, Renaud Justin. "Studying the Dissociation Behaviour of Ionized Non-covalent Complexes with a Cohesive Energetic and Structure Approach." Thesis, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31540.
Full textMenad, Samia. "Assemblage permanent de micro-objets par diélectrophorèse associée à une méthode de couplage covalent." Thesis, Ecully, Ecole centrale de Lyon, 2014. http://www.theses.fr/2014ECDL0037/document.
Full textThe design of micro and nanomaterials with controlled properties requires the development of new bottom- up assembly approaches. The work presented in this manuscript aims to control the formation of aggregates of colloidal particles and cells, with potential applications in the fields of biosensors, microelectronics, optics and tissue engineering. The proposed approach for assembling colloids into organized structures is based on the use of dielectrophoresis, a phenomenon observed when polarizable particles are placed in a non-uniform electric field. One of the drawbacks of this technique is the reversibility of the assemblies thus formed, the cancellation of the electric field causing the redispersion of the colloids. As a solution to this problem, we proposed to use a coupling agent to maintain the cohesion of the structures formed in the liquid medium. In order to better control the dielectrophoretic behavior and the chemical reactions exploited, electrical and chemical characterizations of the manipulated particles were carried out. Moreover, different types of microelectrodes have been studied for the generation of the electric field required for the assembly. A new approach has been developed for the fabrication of transparent micro patterned ITO microelectrodes and their integration in microfluidic systems, based on the exploitation of a thin micro-structured PDMS membrane used as an insulating layer. The method has been applied to the fabrication of "vertical" microelectrodes and of quadrupolar electrode arrays. The latter were used to obtain permanent assemblies of carboxylic acid functionalized, fluorescent, polystyrene particles, by combining negative dielectrophoresis with the use of a chemical coupling agent (Jeffamine). HEK 293 cell aggregates were also produced by negative dielectrophoresis. We have demonstrated that it was possible, under certain conditions, to preserve the permanent character of the cell aggregates after field removal
Fernández, Pérez Héctor. "Towards highly efficent ligands for asymmetric hydrogenations: a covalent modular approach and investigations into bio-inspired supramolecular strategies." Doctoral thesis, Universitat Rovira i Virgili, 2009. http://hdl.handle.net/10803/9041.
Full textLa presente Tesis Doctoral describe también la preparación de nuevos ligandos quirales que pueden comportarse como catalizadores supramoleculares inspirados en el mecanismo de regulación alostérica de los enzimas.
A library of enantiomerically pure P-OP ligands (phosphine-phoshinites and phosphine-phosphites) straightforwardly available in two synthetic steps from enantiopure Sharpless epoxy ethers is reported in the present PhD. Thesis. The "lead" catalyst of the series has proven to have outstanding catalytic properties in the rhodium-catalysed asymmetric hydrogenation of a wide variety of functionalised alkenes. Their excellent performance and modular design makes them attractive for future applications.
This PhD. Thesis also reports the development of a practical route to chiral diphosphine ligands with supramolecular motifs, with potential for allosteric modulation, which we prepared for future catalytic studies.
Serrano, Aparicio Natalia. "Inhibition studies on the human 20S proteasome: molecular insights from a computational approach." Doctoral thesis, Universitat Jaume I, 2022. http://dx.doi.org/10.6035/14122.2022.684242.
Full textPrograma de Doctorat en Química Teòrica i Modelització Computacional
Carlson, David Andrew. "New Approaches To Studying Non-Covalent Molecular Interactions In Nano-Confined Environments." Diss., 2010. http://hdl.handle.net/10161/2973.
Full textThe goal of this work is to develop novel molecular systems, functionalization techniques, and data collection routines with which to study the binding of immobilized cognate binding partners. Our ultimate goal is the routine evaluation of thermodynamic parameters for immobilized systems through interpretation of the variation of the binary probability of binding as a function of soluble ligand concentration. The development of both data collection routines that minimize non-specific binding and functionalization techniques that produce stable ordered molecular systems on surfaces are of paramount importance towards achievement of this goal. Methodologies developed here will be applied to investigating the thermodynamics of multivalent systems.
In the first part of this work, the effect of contact force on molecular recognition force microscopy experiments was investigated. Increased contact forces (>250 pN) resulted in increased probabilities of binding and decreased blocking efficiencies for the cognate ligand-receptor pair lactose-G3. Increased contact force applied to two control systems with no known affinity, mannose-G3 and lactose-KDPG aldolase resulted in non-specific ruptures that were indistinguishable from those of specific lactose-G3 interactions. Thus, it is essential to design data collections routines that minimize contact forces to ensure that ruptures originate from specific, blockable interactions.
In the second part of this work we report the first example of the preparation of stable self assembled monolayers through hydrosilylation of a protected aminoalkene onto hydrogen-terminated silicon nitride AFM probes and subsequent conjugation with biomolecules for force microscopy studies. Our technique can be used as a general attachment technique for other molecular systems.
In the third part of this work we develop novel molecular systems for tethering oriented vancomycin and its cognate binding partner L-Lys-D-Ala-D-Ala to surfaces and AFM tips. Unbinding experiments demonstrated that traditional methods for forming low surface density amine layers (silanization with APTMS and etherification with ethanolamine) provided molecular constructs which displayed probabilities of binding that were too low and showed overall variability too high to use for probabilistic evaluation of thermodynamics parameters. Instability and heat-induced polymerization of APTMS layers on tips and surfaces also prohibited their utility. Formation of Alkyl SAMs on silicon provides a more reliable, stable molecular system anchored by Si-C bonds that facilitates attachment of vancomycin and is capable of withstanding prolonged exposure to heated organic and aqueous environments. It follows that covalent immobilization of KDADA to silicon nitride AFM tips via Si-C bonds using hydrosilylation chemistry will be similarly advantageous. These methods offer great promise for probabilistic evaluation of thermodynamic parameters characterizing immobilized binding partners and will permit unambiguous determination of the role of multivalency in ligand binding, using an experimental configuration in which intermolecular binding and aggregation are precluded.
Dissertation
Shi, Xuesong. "Hydration in non-covalent DNA-drug interactions: The high-pressure approach." 2007. http://link.library.utoronto.ca/eir/EIRdetail.cfm?Resources__ID=478978&T=F.
Full textAlmeida, Diogo Alexandre Fernandes de. "Analysis of Non-Covalent interactions in general classes of materials using a real-space charge density approach." Master's thesis, 2020. http://hdl.handle.net/10316/93927.
Full textNon-covalent interactions have long been known to be responsible for significant mechanisms in biological structures, and have historically lacked a satisfying or intuitive quantum mechanical description. The recently developed NCI index method by Johnson et al [1] fills a gap that existed within topological methods for the visualization of non-covalent interactions [2]. Even following its implementation by some of the original authors on the NCIPLOT software [3, 4], the method itself has not gained much traction in the Physics community, despite its possible and pertinent use in visualizing and describing non-covalent interactions in solids, including novel materials in which this type of interaction is responsible for structural stabilization. The project described in this document aims to bridge this gap between the method and its potential users by implementing it on a significantly simple, fast, and easy to modify Python script which works for several types of systems and takes as input files of the universally known cube format, which can be output by most major quantum chemistry and electronic structure codes. The resulting code is tested on both simple systems and systems of significant interest.[1] Erin R. Johnson, Shahar Keinan, Paula Mori-Sánchez, Julia Contreras-García, Aron J. Cohen, and Weitao Yang. Revealing noncovalent interactions. Journal of the American Chemical Society, 132(18) 6498–6506, may 2010.[2] Christophe Narth, Zeina Maroun, Roberto A. Boto, Robin Chaudret, Marie Laure Bonnet, Jean Philip Piquemal, and Julia Contreras-García. A Complete NCI Perspective: From New Bonds to Reactivity. In Challenges and Advances in Computational Chemistry and Physics, volume 22, pages 491–527. 2016.[3] Julia Contreras-García, Erin R Johnson, Shahar Keinan, Robin Chaudret, Jean-Philip Piquemal, David N Beratan, and Weitao Yang. NCIPLOT: A Program for Plotting Noncovalent Interaction Regions. J. Chem. Theory Comput, 7:625–632, 2011.[4] Roberto A Boto, Francesca Peccati, Chaoyu Quan, Alessandra Carbone, Jean-Philip Piquemal, Yvon Maday, and Julia Contreras-Garcia. NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions. J. Chem. Theory Comput, 16:0, 2020.
Há algum tempo se sabe que interações não-covalentes são responsáveis por mecanismos significativos em estruturas biológicas e, historicamente, careciam de uma descrição quântica intuitiva ou satisfatória. O método `NCI index' desenvolvido recentemente por Johnson et al [1] preenche uma lacuna que existia em métodos topológicos para a visualização de interações não-covalentes [2]. Mesmo depois da sua implementação por alguns dos seus autores originais no software NCIPLOT [3, 4], o método em si não ganhou muita visibilidade na comunidade de Física, apesar do seu uso possível e pertinente na visualização e descrição de interações não-covalentes em sólidos, incluindo novos materiais nos quais este tipo de interação é responsável pela estabilização estrutural. O projeto descrito neste documento visa preencher esta lacuna entre o método e seus potenciais usuários, implementando-o num `script' Python significativamente simples, rápido e fácil de modificar, que funciona para vários tipos de sistemas e toma como `input' ficheiros do formato universalmente conhecido `cube', que pode ser gerado pela maioria dos principais códigos de química quântica e estrutura eletrónica. O código resultante é testado tanto em sistemas simples como sistemas de interesse significativo.[1] Erin R. Johnson, Shahar Keinan, Paula Mori-Sánchez, Julia Contreras-García, Aron J. Cohen, and Weitao Yang. Revealing noncovalent interactions. Journal of the American Chemical Society, 132(18) 6498–6506, may 2010.[2] Christophe Narth, Zeina Maroun, Roberto A. Boto, Robin Chaudret, Marie Laure Bonnet, Jean Philip Piquemal, and Julia Contreras-García. A Complete NCI Perspective: From New Bonds to Reactivity. In Challenges and Advances in Computational Chemistry and Physics, volume 22, pages 491–527. 2016.[3] Julia Contreras-García, Erin R Johnson, Shahar Keinan, Robin Chaudret, Jean-Philip Piquemal, David N Beratan, and Weitao Yang. NCIPLOT: A Program for Plotting Noncovalent Interaction Regions. J. Chem. Theory Comput, 7:625–632, 2011.[4] Roberto A Boto, Francesca Peccati, Chaoyu Quan, Alessandra Carbone, Jean-Philip Piquemal, Yvon Maday, and Julia Contreras-Garcia. NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions. J. Chem. Theory Comput, 16:0, 2020.