Dissertations / Theses on the topic 'Ligand design'

The known ruthenium pincer complex RuCl(eta3-dcpx)(PPh 3) (7) (PCP = eta3-2,6-(PCy2CH 2)2C6H3) was transformed into several different hydride products under standard transfer hydrogenation conditions. In situ 31P NMR analysis during thermolysis of 7 in basic isopropanol permitted identification of RuH(eta3-dcpx)(PPh 3)(N2) (8a/b), RuH(eta3-dcpx)(PPh 3) (10), and RuH(eta3-dcpx)(PPh3 )(H2) (9a/b). A spectroscopically unobservable species, Ru(H)2[eta2-PC(H)P] (12), is proposed as the active species in transfer hydrogenation catalysis. The novel precatalyst, RuCl(eta3-dcpx)(py)2 ( 14), which may provide a more active catalyst, was synthesized and characterized. Several primary and secondary phosphine complexes of ruthenium were synthesized and tested for their activity in catalytic transfer hydrogenation. Of these, only the bulky HPCy2 ligand in RuCl2(HPCy2) 4 (18a/b) provided high catalytic activity. Reaction of RuCl2(PCy3)2(=CHPh) (24) with HPCy2 transforms it cleanly to 18a, potentially opening new opportunities in tandem catalysis. (Abstract shortened by UMI.)

This thesis involves the design, synthesis and testing of organic hydrophobic ligands. They would act as co-collectors in froth flotation processes to enhance the recovery of sulfidic minerals which have undergone some oxidation on processing and are not efficiently collected by the commercial reagents used in froth flotation. Strong and selective binding to iron(III) oxide/hydroxide surfaces, e.g. goethite, over unwanted silicaceous material was considered essential criteria for such new cocollectors. A general overview of froth flotation processes is given in Chapter 1 as well as a description of the analytical techniques used in this thesis and the features that the ligands must have to act as co-collectors. On the basis of the strong binding to iron(III) surfaces of the organic ligand Irgacor 419®, used commercially as a corrosion inhibitor for iron, this compound was studied as a potential co-collector. Adsorption isotherms were determined by UV-Vis spectroscopy for two carboxylic acids that may also bind strongly to goethite, the results of which are discussed in Chapter 2. Chapter 3 involves the measurement of the strength of binding of one the most widely used type of collectors for sulfide ores, potassium ethyl xanthate. Complications in the analysis of materials in solution by both ICP-OES and UV-Vis spectroscopy arose due to the instability of potassium ethyl xanthate in solution, making determination and interpretation of isotherms difficult. The determination of adsorption isotherms for 2-mercaptobenzothiazole, which showed weak binding to goethite as well as to silica, and the mode of binding of 2-mercaptobenzothiazole on copper(I) surfaces is reported in Chapter 4. A crystal structure was obtained in which four units of 2-mercaptobenzothiazole bridge two nickel atoms through the nitrogen atom and the exocyclic sulfur and is considered as a model for binding to sulfidic minerals. Chapter 5 looks at the strength of binding to goethite and silica of various hydroxamic acids. Benzohydroxamic acid was initially selected for study since hydroxamates are known to act as collectors for oxidized materials. Unpredictably, benzohydroxamic acid showed strong binding to a goethite surface and did not release any iron from the surface into solution, which would have been predicted due to its known strong chelating abilities to iron(III). The X-ray structure determination of the first example of a dinuclear Fe(III) hydroxamate complex showed this to have -oxo bridge formed by the hydroxamate unit and supports multisite attachment between this ligand and the surface, as suggested by adsoption isotherms. Simple models based on this dinucleating motif provide plausible modes of multisite attachment to a goethite surface. Competitive binding studies provided a way of ranking the ability to bind to goethite of acetohydroxamic acid, which was not suitable for analyses by either ICP-OES or UV-Vis spectroscopy. Of the ligands studied in this chapter acetohydroxamic acid was found to bind most strongly to goethite followed by benzohydroxamic acid. In Chapter 6, the attachment to goethite and silica of a series of phosphonic acids is investigated. All show a very high binding strength to goethite. Froth flotation experiments at a laboratory scale are described in Chapter 7. The types of ligand that showed strong binding to goethite in adsorption isotherms experiments were tested as co-collectors in different ores and conditions. There is not a simple correlation between adsorption isotherm data and flotation performance as co-collectors because other factors, besides strength of binding, affect the system. Benzohydroxamic acid was the ligand that increased the grade/recovery of the process in all the cases studied. Irgacor 419® enhances the grade/recovery curve for Palabora ore and phenyl malonic acid for Kennecott ore. These results support the original proposition that it may be possible to increase the recovery of oxidized particles substantially by using a blend of collectors which includes a compound to target the oxidized sites.

This doctoral thesis focuses on the synthesis of new ligands and their application in two types of catalytic process: a) palladium catalysed carbonylation reactions and b) asymmetric reactions (hydrogenation of challenge substrates and C-C bond formation). In the first part of the thesis, the synthesis of a family of new diphosphine ligands and their application in Pd-catalysed carbonylation processes is described. These ligands were first used in the Pd-catalysed methoxycarbonylation of ethane, achieving high activity and selectivity. A mechanistic study on these catalytic systems revealed the resting state of this process. The new ligands were also applied in the aminocarbonylation and double-carbonylation of aryl iodides, achieving high level of chemoselectivity in each case. NMR studies on these systems led to the discovery and development of the first phosphine-free Pd-catalysed double-carbonylation of aryl iodides where the base used in the process revealed to also play a key role as ligand and nucleophile. The second part of this thesis describes the synthesis of new phosphino-imidazoline ligands and their application in the Ir-catalysed asymmetric hydrogenation of unfunctionalised olefines and imines achieving moderate enantioselectivities. These ligands were also applied in the Pd-catalysed allylic substitution reactions, achieving excellent enantioselectivities for a wide range of substrates and nucleophiles. An efficient recovery of the catalytic system was carried out by anchoring a phosphino-imidazoline ligand onto a polymer support or using ionic liquids as reaction medium.

Elastase is irreversibly inhibited by compounds incorporating a β-lactam ring and this thesis describes structural studies on three classes of β-lactam inhibitor. The mechanism of inhibition begins with nucleophilic attack by the catalytic serine on the carbonyl which is at position 2 of all the β-lactams. In all cases this results in the opening of the ring between position one and two and the departure of the position four substituents. X-ray crystal structures and mass spectra obtained of elastase in complex with each of the ligands described the bound products of each reaction. β-lactams having geminal diethyl groups at position 3 of the ring were proven to react by a different mechanism to those with a hydroxyl ethyl at position 3. Hydroxy ethyl ligands are proposed to result in amore stable bound product. A ligand which had an ethyl group attached by a double bond at position 3 was found to be hydrolysed by the enzyme to give a breakdown product which remains non-covalently bound in the active site. A crystal structure of the non-covalently bound product was determined. The determination of 3-D structures of elastase with gold triethyl-phosphine and rhenate is also reported. Factor XIII is the last enzyme in the blood coagulation cascade, stabilising blood clots by cross-linking fibrin. It is a transglutaminase, linking a lysine from one peptide substrate to a glutamine from the other via e(γ-glutamyl)lysyl isopeptide bonds. In plasma, factor XIII exists in the inactive form as a heterotetramer, having two A subunits and two B subunits. Upon activation the two B subunits fall away and the A-A dimer performs the catalysis. The activation process also involves an unknown conformational change and thrombin cleavage which allows the departure of an activation peptide. Attempts made to purify the active form of the enzyme for crystallisation are described. A crystal structure of the inactive form of factor XIII has been used as the basis for computer modelling of the interaction of peptide ligands and the active form of the enzyme.

La preparación de nuevos ligandos quirales P-OP (fosfina-fosfinitos y fosfina-fosfitos), fácilmente preparados con una estrategia sintética en dos etapas desde una aproximación covalente, es descrita en la presente Tesis Doctoral. El mejor catalizador de la serie ha demostrado tener propiedades catalíticas excelentes en la hidrogenación asimétrica catalizada por rodio de una amplia variedad de olefinas funcionalizadas. El resultado excelente y el diseño modular de los ligandos sintetizados hacen éstos muy atractivos para futuras aplicaciones.<br/>La 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.<br>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.<br/>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.

For the purpose of incorporating indoles into organometallic complexes for catalysis, as well as in the generation of new heterocyclic systems, various reactions have been carried out at C2, C6 and C7 of the indole system. In order to achieve this, 3-substituted 4,6-dimethoxyindoles and 6-hydroxy- 4-methoxyindoles were necessary as starting materials. Consequently, a lithium-bromide-templated one-pot procedure for the synthesis of some 3-substituted 4,6-dimethoxyindoles and a selective demethylation procedure for 3-substituted 6-hydroxy-4-methoxyindoles were developed. Various kinds of novel methylene-bridged bi-, tri-, and tetradentate pyridyl-indole ligands were synthesised via Vilsmeier-Haack, Friedel-Crafts or electrophilic addition reactions on the indole heterocycle. However, their metal complexing properties were generally weak and variable. Nevertheless, some of the tridentate pyridylindole ligands showed strong anion binding to halides, whereas a remarkable ligand transformation occurred with a bidentate 2-pyridylindole ligand and zinc(II), giving a substituted indolo[2,3-c]pyrrolo-[3,2,1-ij]quinoline system. Two new types of tetradentate Schiff base ligands were prepared from 2-formyl-indoles and 7-formyl-6-hydroxyindoles, and diamines. These preformed ligands were reacted with first- and second-row transition metals to give neutral metal complexes. Novel heterocyclic systems such as 4H-pyrrolo[3,2,1-ij]quinolines, 3H-pyrrolo-[1,2-a]indoles, and 1H-furo[2,3-g]indoles were synthesised from 2-formyl-, 7-formyl-, and 6-hydroxyindoles, utilising mainly intra-molecular Wittig reactions, Claisen-Schmidt condensations or acid- and base-catalysed cyclisations. A common feature of the prepared 4H-pyrrolo[3,2,1-ij]quinolines and 3H-pyrrolo-[1,2-a]indoles was their intense fluorescent character, which was examined as well.

La indústria química empra la catàlisi homogènia com eina en la síntesi de diversos productes, des de plàstics fins a medicaments. Normalment els catalitzadors homogenis són complexos mononuclears amb lligands difosfines que generalment presenten una coordinació cis. Aquesta tesi esta enfocada en el desenvolupament i aplicació en catàlisi de nous lligands nitrogenats que preferiblement formen complexos de coordinació trans o dinuclears. El complexos de coordinació amb lligands bidentats s’aplicaren en diverses reaccions catalítiques com l’hidrogenació asimètrica d’alquens; l’ hidrosililació asimètrica d’acetofenona catalitzades per rodi i l’oxidació de meso-diols catalitzada per coure o ferro. Les diferents famílies de complexos dinuclears de ferro i zinc, preparats amb els lligands tetradentats, van aplicar-se com a catalitzadors en diverses transformacions catalítiques. Com per exemple la síntesi carbonats cíclics a partir d’epòxids i diòxid de carboni. També es va explorar l’oxidació d’enllaços C–H amb els complexos de ferro.<br>Homogeneous catalysis is a useful synthetic tool in the chemical industry. Several products, for instance in fine chemicals were prepared by metal-catalyzed reactions. Usually the catalysts are mononuclear complexes containing diphosphine ligands generally coordinated in a cis fashion. This thesis focused in the development and application in catalysis of new nitrogen ligands which form trans or dinuclear metal complexes. Coordination complexes with bidentate ligands were applied in several metal catalyzed reactions, for example asymmetric alkene hydrogenation and asymmetric acetophenone hydrosilylation with rhodium. They were also applied in the oxidation of meso-diols with copper and iron. Multinuclear complexes were prepared for iron and zinc with tetradentate ligands. These complexes were applied in different catalytic transformations, for instance, the synthesis of cyclic carbonates from carbon dioxide and epoxides. C–H catalytic oxidation was explored with the dinuclear iron complexes.

This thesis describes several cyclopentyl linked enamide phosphine ligands. Reactivity and mechanistic studies using coordination compounds featuring these ligands enable exploration of ligand cooperativity. Despite complex behavior in solution due to tautomerization, coordination of (NPN)DMP/DIPPH₂ to Rh generates RhCl{(NPN)DMP/DIPPH₂}(COE). Synthesis of RhCl{(NPN)DMP/DIPPH₂}(CO) and RhHCl₂{(NPN)DMP/DIPPH₂} is possible. NMR spectroscopy and in certain cases X-ray analysis establishes the diimine tautomer of the ligand coordinates to Rh in each case. Enamide phosphine complexes, Ir{(NP)DIPP}(COD) and Ir{(NP)DMP}(COD) are synthesized from simple imine phosphine ligands. Ir{(NP)DIPP}(COD) reacts with H₂ or PriOH to form [IrH₃{(NP)DIPPH}]₂. The imine tautomer of the ligand coordinates to Ir. Treating [IrH₃{(NP)DIPPH}]₂ with CO generates Ir{(NP)DIPP}(CO)₂. A proton from the imine ligand of [IrH₃{(NP)DIPPH}]₂ combines with an Ir hydride to release H₂. Observation of three intermediates, involved in conversion of [IrH₃{(NP)DIPPH}]₂ to Ir{(NP)DIPP}(CO)₂, suggests that tautomerization of the dissociated arm is involved in cooperative H₂ loss. Four imine phosphine ligands (R(NP)R'H), where the N-aryl groups (R) and the groups attached to P(R') are varied, are synthesized. Combining each ligand with RuHCl(PPri₃)₂(CO) and KOBut generates four enamide phosphine complexes: RuH{R(NP)R'}(PPri₃)(CO). Reacting RuH{R(NP)R'}(PPri₃)(CO) with H₂ generates RuH₂{R(NP)R'H}(PPri₃)(CO). The imine tautomeric form of the ligand coordinates to Ru in all four cases. The R' groups influence the rate of reaction and percent conversion to RuH₂{R(NP)R'H}(PPri₃)(CO). The mechanism for H₂ activation is explored using RuH{Pri(NP)Pri}(PPri₃)(CO). An intermediate is identified as RuH₂(H₂){Pri(NP)PriH}(PPri₃)(CO). The T₁,min value of a ¹H NMR resonance at δ -7.2 is 22 ms at 238 K (measured to 400 MHz), consistent with a Ru dihydrogen dihydride complex. The N donor of the enamine tautomeric form of the ligand is protonated by H₂ or D₂ and has dissociated from Ru. Tautomerization of the dissociated arm is involved in formation of the final product. Certain factors inhibit alcohol dehydrogenation catalysis for Ir{(NP)DIPP}(COD) and RuH{Pri(NP)Pri}(PPri₃)(CO). Two tridentate enamide phosphine ligands are developed in an effort to generate a catalyst. These ligands enable synthesis of RuH{(PNN)But}(CO) and RuH{(PNN)Pri}(CO). Exposing RuH{(PNN)But}(CO) to 1000 equivalents of benzyl alcohol yields a TON of 13 and TOF of 0.6 h-¹ after 22 hours. Nearly identical results are obtained for RuH{(PNN)Pri}(CO).<br>Science, Faculty of<br>Chemistry, Department of<br>Graduate

The chemistry of the tetrameric low-valent aluminium compoud (Cp*Al)4 (Cp* = 1,2,3,4,5- pentamethylcyclopentadienyl) is relatively undeveloped compared to its monomeric cousin dippNacNacAl (dippNacNac = 2,6-diisopropylphenyl-β-diketiminate). Given that the former can be formed by the reductive elimination of Cp*H from Cp*2AlH, a process common to transition metals yet rare with light main-group elements, using the Cp* ligand could unlock an abundance of unexpected reactivity for aluminium. An overview of the literature regarding the synthesis and reactivity of low oxidation state aluminium compounds is provided in chapter 1, as well as an introduction to relevant magnesium chemistry for this work. Chapter 2 studies the mechanism of C-H reductive elimination from Cp*2AlH to form (Cp*Al)4, and the properties which allow reductive elimination to take place are revealed. A transition state is identified where the Cp* group has a higher hapticity than in the starting material, a process which is thought to enable the reductive elimination. Using this insight, aluminium hydride and halide complexes featuring 9-methylfluorenyl ligands are synthesised and reduction of the aluminium centre is investigated. The reactivity of (Cp*Al)4 is considered in chapter 3 of this thesis. The formal cycloaddition reaction between (Cp*Al)4 and diphenylacetylene produces a Lewis acidic 1,4- dialuminacylohexadiene derivative. The inner Al2C4 ring of this complex is stable, with onward reactions happening at the complex's periphery. Insertion reactions in the Al-CCp* bonds are observed with unsaturated C-N species. With 2,6-dimethylphenylisonitrile the Al2C4 complex forms a zwitterionic aluminate, featuring a stable carbocation derived from the Cp* group. An amidinate complex with an unusual Cp* backbone is formed from the insertion of carbodiimides into the Al-CCp* bond of the 1,4-dialuminacyclohexadiene. Extending this, the insertion of carbon dioxide into the same bond is explored. The use of amidine ligands is common in main-group chemistry, however literature relating to the related phosphaamidinate ligands ([RPC(R)NR]-) is only reported sporadically. They have not been applied in a general manner to main-group chemistry thus far. Chapter 4 describes the synthesis of five new phosphaamidinate pro-ligands where the steric bulk of both the phosphorus and nitrogen components is increased systematically. To evaluate these new ligands, their coordination chemistry with magnesium was investigated. Three examples of heteroleptic LMgnBu (L = phosphaamidinate) complexes are synthesised, which all show high activity for the ring-opening polymerisation of racemic lactide. The resulting polylactide chains show good molecular weights and polydispersity indices. The synthesis of homoleptic L2Mg complexes is also described. Chapter 5 applies these new phosphaamidinate ligands to aluminium chemistry. An aluminium hydride species is isolated, which is shown to form via a probable lithium aluminate intermediate. The lifetime of this intermediate is found to be heavily dependent on the reaction solvent.

Thesis (Ph.D.)--University of Tennessee Health Science Center, 2008.<br>Title from title page screen (viewed on February 2, 2009). Research advisor: Richard E. Lee, Ph.D. Document formatted into pages (xviii, 238 p. : ill.). Vita. Abstract. Includes bibliographical references (p. 167-186).

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.

This thesis describes the development of new catalytic systems based upon iron complexes and their reactivity toward ethylene. First, we focused our interest on the synthesis of iron(III) precursors chelated by monoanionic ligand. Those complexes were obtained either by reaction of the monoanionic ligand with FeCl3 or through oxidation of the iron(II) complex. The second reaction led to binuclear complexes. Then, another aim of the thesis was to design new well-defined cocatalysts for the activation of iron complexes. The study of the reaction between an alcohol and the trimethylaluminum allowed us to reach this aim. Aluminum complexes adopted either a binuclear framework or a trinuclear one, depending on the nature of alcohol reagent. Besides this work, new iron(II) and nickel(II) complexes chelated by imino-imidazole ligands bearing a pendant donor function L were synthesized. All complexes have been evaluated for the oligomerization of ethylene in the presence of EtAlCl2 or MAO as cocatalyst. Only nickel complexes were active toward ethylene transformation.

Rheumatoid arthritis is a debilitating disease for which there is no cure. Copper has been used for centuries to alleviate the inflammation associated with the disease. The aim of this research was to design and test new ligands which are able to promote the percutaneous absorption of copper and/or mobilize endogenous copper reserves. Formation constants of H+, Cu(II), Ni(II) and Zn(II) with five low molecular ligands 2-((2-aminoethyl)amino)-N-(pyridin-2- ylmethyl)acetamide) [H(555)NH2], 2-((2-dimethyl-amino)ethyl)amino)-N-(pyridin-2-ylmethyl) acetamide [H(555)NMe2], N-(2-aminoethyl)-N'-(pyridin-2-ylmethyl)ethanediamide [H2(555)NH2], 3-(2-aminoacetamido)-N-(pyridin-2-ylmethyl)propanamide [H2(565)NH2], 3-amino-N-(pyridin-2-lmethyl)-propanamide [H(56)NH2] were measured at 25±0.01oC and at an ionic strength of 0.15M (NaCl) using glass electrode potentiometry. The structures of the different Cu(II) species formed with these ligands were investigated using ultraviolet-visible (Uv-visible), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography as well as molecular mechanics calculations. The Uv-visible spectra obtained for the different species in solution were typical of tetragonally distorted Cu(II) complexes. The active binding sites were identified as the pyridine nitrogen, the amide nitrogen and the terminal amino group. The pyridine nitrogen was involved in coordination first, followed by the amide and then the terminal amine groups. The X-ray crystal structure of two of the Cu(II) complexes were solved; one formed a rectangular pyramidal geometry and the other a distorted square planar geometry. Molecular mechanics was used to determine the lowest energy conformation of different possible geometries. Since the preferred route of administration is through the skin, the rate of dermal absorption and the bioavailability of copper are important. For this reason, the drugs were designed so that they could be administered dermally and be selective for Cu(II) so that they do not affect the speciation of other metal ions in blood plasma. Speciation calculations using a blood plasma model were used to estimate the complexing ability of the ligands in vivo. This result showed that [H(555)NH2] was the best at mobilising copper in vivo.

The water-to-oxygen redox couple, H2O/O2, powers our aerobic life through the fundamental processes of natural photosynthesis and cellular respiration. Despite its vital role, any failure of this four-electron mechanism turns out to release O2-derived toxic radicals, inducing a severe oxidative damages of any synthetic and biological materials exposed to the aerobic risk. The aerobic formation of ROS is due to oxygen reduction in-vivo, generating the superoxide anion (O2•–), hydrogen peroxide (H2O2), and the hydroxyl radical (HO•). ROS give rise to fast, barrier-less, short-range and non-selective oxidation steps, being responsible for the “oxidative stress”, a key factor for cellular death, organ failure and aging diseases. In addition photo-oxidative stress is one key factor limiting plant productivity, i.e. bio-mass and food yield. Noteworthy, ROS-forming mechanisms are also lethal for the stability of bio-inspired materials designed for artificial photosynthesis in vitro. The biological defense against ROS-induced cellular damage stems from the combined action of “anti-oxidant” metallo-enzymes, as superoxide dismutase (SOD), and catalase (CAT). A detoxification cascade occurs via SOD-induced dismutation of O2•– into O2 and H2O2 which is then converted by CAT into H2O and O2 again. In this thesis will be presented the design of a set of novel anti-oxidant catalysts, based on different metal centers, that can emerge by the engineering of a synzyme with integrated SOD/CAT activity able to mimic both the enzymes activities and efficiently perform a complete ROS scavenging also in biological-like solution. The activity of the synzymes will be also tested in water splitting processes to perform both the water oxidation than the proton reduction reactions in water at neutral pH, a key feature to obtain sustainable energy sources from water. The obtained results will be divided in four main chapters: - Chapter 2: coupling of a polycationic Mn(III)-porphyrin, with a dinuclear Mn2(II,II)L2 core results in a dual Superoxide Dismutase (SOD) and Catalase (CAT) functional analog, Mn2L2Pn+, enabling a detoxification cascade of the superoxide anion and hydrogen peroxide into benign H2O and O2. The SOD/CAT artificial manifolds, joined in one asset, exhibit a peak catalytic performance under physiological conditions, with log kcat(O2•–) ≥ 7 and kcat(H2O2)/KM = 1890. The dual-enzyme (di-zyme) concept allows for a unique, built-in-self-protection, against the irreversible bleaching of the porphyrin unit, (> 75% protection), readily induced by H2O2 (200 μM, 20 equivalents, in buffer solution, pH=7.8). We show herein that incubation of the photosynthetic green algae, Chlamydomonas reinhardtii, with the synthetic di-zyme (as low as 0.1 μM), prevents H2O2 accumulation under high-light illumination conditions, thus providing an efficient anti-oxidant surveillance and photo-protection. - Chapter 3: dinuclear Cu(II)2L2 catalysts were synthesized and studied for their SOD/CAT activity. The goal of this study was to demonstrate that with a proper ligand set, is it possible tune the reactivity of an harmful metal like copper, turns it to a benign anti-oxidant system. The dinuclear copper complexes show SOD activity with logkcat up to 7.55 and CAT activity with rate of O2 production up to 4.4 μM/s. Kinetic studies of the process of hydrogen peroxide dismutation show also an evolution of the catalyst during the catalytic turnover. No evidence of oxidation of external substrates was also confirmed as consequence of the sacrificial internal scavenger. - Chapter 4: novel Fe(III)L, Fe(III)2L2 and Co2(II)L2 complexes have also been isolated. Preliminary results indicate that a multi-redox manifold is available for both species, however with scarce activity as ROS scavenger. These complexes show instead an interesting activity in the water oxidation process. In addition the anodic waves observed in reduction are promising for catalytic proton reduction processes performed by using directly water as proton source. - Chapter 5: application of oxygen evolving catalysts within functional materials has been explored in the field of porous membranes. This novel stimuli-responsive strategy against the irreversible fouling of porous materials and surfaces is based on the molecular design of catalytic pore walls that foster a chemo-mechanical, self-cleaning behaviour under neutral pH and mild conditions of pressure and temperature. To this aim, the catalase-like behaviour of the tetra-ruthenium substituted polyoxometalate, has been exploited for in-pore oxygen evolution so to induce an active fluid mixing and the displacement of foulant particles. The present study includes the fabrication of hybrid polymeric films with porous architecture embedding the tetra-ruthenium catalyst as artificial catalase to guarantee the material self-defence against pore occlusion and oxidative damage with aqueous H2O2 as mild chemical effector.<br>La coppia redox acqua-ossigeno, H2O/O2, alimenta la nostra vita aerobica attraverso i processi fondamentali della fotosintesi naturale e della respirazione cellulare. Nonostante il suo ruolo fondamentale, qualsiasi errore in questo meccanismo a quattro elettroni rilascia radicali O2-derivati tossici, inducendo gravi danni ossidativi ai materiali sintetici e biologici esposti. La formazione aerobica di ROS è dovuta alla riduzione dell'ossigeno in vivo, generando l'anione superossido (O2•-), perossido di idrogeno (H2O2) ed il radicale idrossile (HO•). I ROS danno origine ad una veloce ossidazione, senza barriere, a corto raggio e non selettiva, responsabile dello "stress ossidativo", un fattore chiave per la morte cellulare, insufficienza di organi e le malattie dell'invecchiamento. Inoltre lo stress foto-ossidativo è un fattore chiave che limita la produttività di piante, bio-masse e rese alimentari. Meccanismi ROS indotti sono anche letali per la stabilità dei materiali bio-ispirati progettati per fotosintesi artificiale in vitro. La difesa biologica contro i danni cellulari ROS indotti deriva dall'azione combinata di metallo-enzimi "anti-ossidanti", come la superossido dismutasi (SOD) e la catalasi (CAT). Il processo di disintossicazione avviene tramite la dismutazione SOD indotta di O2•- in O2 e H2O2 che viene poi convertita nuovamente da CAT in H2O e O2. In questa tesi verrà presentata la progettazione di una serie di nuovi catalizzatori antiossidanti, basati su differenti centri metallici, che possono derivare dalla progettazione di sinzimi con integrata attività SOD/CAT in grado di imitare entrambi gli enzimi ed eseguire efficientemente una completa rimozione di ROS in condizioni simili a quelle biologiche. L'attività dei sinzimi sarà testata inoltre nei processi di scissione dell'acqua per effettuare sia il processo di ossidazione dell'acqua che la riduzione di protoni in acqua a pH neutro, una caratteristica fondamentale per l’ottenimento fonti energetiche sostenibili dalla acqua. I risultati ottenuti saranno divisi in quattro capitoli principali: -Capitolo 2: l’unione di una porfirina policationica di Mn(III), con un sistema dinucleare Mn2(II,II)L2 risulta in un duplice analogo funzionale di superossido dismutasi (SOD) e catalasi (CAT), Mn2L2Pn+, consentendo una disintossicazione a cascata dell'anione superossido e del perossido di idrogeno in H2O e O2. I complessi SOD/CAT artificiali, uniti in un’unica struttura, mostrano un picco delle performance catalitiche in condizioni fisiologiche, con logkcat(O2•-) ≥ 7 e kcat(H2O2)/KM = 1890. Il concetto di doppio-enzima (di-zima) consente una autoprotezione unica, contro la degradazione irreversibile dell'unità porfirinica, (> protezione 75%), indotta rapidamente da H2O2 (200 μM, 20 equivalenti, in soluzione tampone, pH=7.8). Qui viene dimostrato che l'incubazione delle alghe verdi fotosintetiche, Chlamydomonas reinhardtii, con il di-zima sintetico (a concentrazioni fino a 0,1 μM), previene l'accumulo di H2O2 in condizioni di elevata illuminazione, fornendo così un efficiente azione anti-ossidante e foto-protettiva. -Capitolo 3: sono stati sintetizzati e studiati dei catalizzatori binucleari Cu(II)2L2 per la loro attività SOD/CAT. L'obiettivo di questo studio è stato quello di dimostrare che con una serie di leganti adeguati, è possibile regolare la reattività di un metallo dannoso come il rame, trasformandolo in un sistema anti-ossidante. I complessi binucleari di rame mostrano un’attività SOD con logkcat fino a 7,55 e un'attività CAT con velocità di produzione di O2 fino a 4,4 μM/s. Studi cinetici del processo di dismutazione dell’acqua ossigenata mostrano una evoluzione del catalizzatore durante il turnover catalitico. Nessuna evidenza dell’ossidazione di substrati esterni è stata osservata grazie alla presenza di una funzionalità interna sacrificale. - Capitolo 4: sono stati isolati dei nuovi complessi Fe(III)L, Fe(III)2L2 e Co2(II)L2. I risultati preliminari indicano che le specie sono in grado di sostenere processi multi-elettronici, ma con scarsa attività nell’eliminazione di ROS. Questi complessi mostrano invece un'attività interessante nel processo di ossidazione dell'acqua. Inoltre le onde anodiche osservate in riduzione sono promettenti nel processo di riduzione catalitica dei protoni eseguito utilizzando direttamente acqua come fonte di protoni. - Capitolo 5: è stata esplorata l’applicazione nel campo dei materiali funzionali di catalizzatori che sviluppano ossigeno all'interno di membrane porose. Questa nuova strategia stimolo-risposta contro l'incrostazione irreversibile di materiali porosi e superfici si basa sulla progettazione molecolare di pori con pareti catalitiche che esibiscono proprietà autopulenti chemo-meccaniche a pH neutro e in condizioni blande di temperatura e pressione. A questo scopo, l’attività di catalasi di un poliossometallato tetra-rutenio sostituito, è stata sfruttata per lo sviluppo di ossigeno dai pori in modo da indurre una miscelazione attiva del fluido e la rimozione delle particelle sporcanti. Il presente studio prevede la realizzazione di film polimerici ibridi con un’architettura porosa contenenti il catalizzatore di tetra-rutenio come catalasi artificiale per garantire al materiale un meccanismo di auto-difesa contro l’occlusione dei pori e i danni ossidativi, impiegando una soluzione acquosa di H2O2 come stimolo chimico.

Indications that existing parameter sets of extended Linear Interaction Energy (LIE) models are transferable between lipases from Rhizomucor Miehei and Thermomyces Lanigunosus in complex with a small set of vinyl esters are demonstrated. By calculat- ing energy terms that represents the cost of forming cavities filled by the ligand and the complex we can add them to a LIE model with en established parameter set. The levels of precision attained will be comparable to those of an optimal fit. It is also demonstrated that the Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods are in- applicable to the problem of calculating absolute binding energies, even when the largest source of variance has been reduced.

In the last decades, the applications of computational methods in medicinal chemistry have experienced significant changes which have incredibly expanded their approaches, and more importantly their objectives. The overall aim of the present research project is to explore the different fields of the modelling studies by using well-known computational methods as well as different and innovative techniques. Indeed, computational methods traditionally consisted in ligand-based and the structure-based approaches substantially aimed at optimizing the ligand structure in terms of affinity, potency and selectivity. The studies concerning the muscarinic receptors in the present thesis applied these approaches for the rational design of novel improved bioactive molecules, interacting both in the orthosteric (e.g., 1,4-dioxane agonist) and in the allosteric sites. The research includes also the application of a novel method for target optimization, which consists in the generation of the so-called conformational chimeras to explore the flexibility of the modelled GPCR structures. In parallel, computational methods are finding successful applications in the research phase which precedes the ligand design and which is focused on a detailed validation and characterization of the biological target. A proper example of this kind of studies is given by the study regarding the purinergic receptors, which is aimed at the identification and characterization of potential allosteric binding pockets for the already reported inhibitors, exploiting also innovative approaches for binding site predictions (e.g., PELE, SPILLO-PBSS). Over time, computational applications felt a rich extension of their objectives and one of the clearest examples is represented by the ever increasing attempts to optimize the ADME/Tox profile of the novel compounds, so reducing the marked attrition in drug discovery caused by unsuitable pharmacokinetic profiles. Coherently, the first and main project of the present thesis regards the field of metabolism prediction and is founded on the meta-analysis and the corresponding database called MetaSar, manually collected from the recent specialized literature. This ongoing extended project includes different studies which are overall aimed at developing a comprehensive method for metabolism prediction. In detail, this Thesis reports an interesting application of the database which exploits an innovative predictive technique, the Proteochemometric modelling (PCM). This approach is indeed at the forefront of the latest modelling techniques, as it perfectly fits the growing request of new solutions to deal with the incredibly huge amount of data recently produced by the “omics” disciplines. In this context, MetaSar represents an alternative and still appropriate source of data for PCM studies, which also enables the extension of its fields of application to a new avenue, such as the prediction of metabolism biotransformation. In the present thesis, we present the first example of these applications, which involves the building of a classification model for the prediction of the glucuronidation reaction. The field of glucuronidation reactions is exhaustively explored also through an homology modelling study aimed at defining the complete three-dimensional structure of the enzyme UGT2B7, the main isoform of glucuronidation enzymes in humans, in complex with the cofactor UDPGA and a typical substrate, such as Naproxen. The paths of the substrate entering to the binding site and the egress of the product have been investigated by performing Steered Molecular Dynamics (SMD) simulations, which were also useful to gain deeper insights regarding the full mechanism of action and the movements of the cofactor.

Parmi la vaste classe des complexes de coordination moléculaire, certains composés présentent des propriétés magnétiques, pour un environnement de coordination approprié. Par exemple, ces propriétés incluent le comportement de molécule aimant, lorsque qu'il y a une barrière d'énergie à l'inversion de l'aimantation, ou des propriétés de bit quantique lorsque la dégénérescence de l'état fondamental est complètement levée. Combiner ces propriétés magnétiques avec d'autres, comme la luminescence ou la commutabilité magnétique dans des matériaux multifonctionnels est particulièrement intéressant. En effet, des applications telles que la manipulation et le stockage d'information, l'information quantique, les dispositifs spintroniques, les capteurs chimiques ou les micro-thermomètres peuvent être envisagées. Bien que prometteuse, la conception de tels complexes moléculaires magnétiques répondant à des stimuli externes représente un défi à la fois au niveau de la synthèse et au niveau de l'analyse des composés. Les ligands pontants redox-actifs sont connus comme unités de construction pour la conception de complexes polynucléaires avec des interactions d'échange ajustables entre les centres magnétiques. Précédemment, notre groupe a contribué à l'émergence de la famille des composés moléculaires construits autour du ligand non-innocent hexahydroxytriphénylène (HHTP), avec un complexe trinucléaire à base de nickel montre des propriétés prometteuses pour la modulation redox du comportement magnétique. Le ligand HHTP est particulièrement intéressant car il possède sept états redox théoriques, passant, via des événements monoélectroniques successifs, de l'état tris-quinone à l'état tris-catécholate. Dans cette thèse, l'accent est mis sur les complexes de coordination conçus autour du ligand HHTP. Leur synthèse est développée, leurs différents états redox sont isolés et leurs propriétés magnétiques sont étudiées à l'état solide par magnétométrie SQUID. Le comportement magnétique attendu est une modulation on/off de l'interaction d'échange entre les centres magnétiques, en fonction de la présence (ou absence) d'électrons non appariés sur le HHTP. Des complexes trinucléaires de nickel et de cobalt, ainsi qu'un dimère hexanucléaire de nickel avec le ligand HHTP sont rapportés. L'étude des différents états redox isolés met en évidence la modulation des propriétés magnétiques par le commutateur redox. Le comportement observé de commutation du comportement magnétique via le switch redox est rationalisé par des calculs ab initio, révélant la structure électronique du HHTP et les mécanismes de l'interaction de spin en son sein. En outre, il est fait état d'explorations ayant pour but de synthétiser des complexes trinucléaires à base de lanthanides autour du ligand HHTP et des complexes binucléaires autour du ligand chloroanilate<br>Among the large class of molecular coordination complexes, some compounds exhibit magnetic properties, given a suitable coordination environment of their metallic ions. For instance, these properties can be the single molecule magnet behavior, when there is an energy barrier to the reversal of the magnetization, or qubit properties when the degeneracy of the ground state is fully lifted. Combining these magnetic properties with others like luminescence or magnetic switchability into multifunctional materials is of interest for applications such as, data manipulation and storage, quantum information, spintronic devices, chemisensors or microthermometers. Although very promising, designing such magnetic molecular complexes that respond to external stimuli is both a synthetic and analytical challenge. Redox-active bridge ligands are well-known as building blocks to design polynuclear complexes with tunable exchange interaction between magnetic centers. Previously our group contributed to the emerging family of compounds based on the hexahydroxytripenylene (HHTP) non-innocent ligand with a trinuclear nickel-based complex showing promising magneto-redox coupled properties. The HHTP ligand is particularly interesting as it has seven theoretical redox states going, through successive monoelectronic events, from the tris-quinone to the tris-catecholate state. In this work the focus is on coordination complexes designed around the HHTP ligand. Their synthesis is developed, isolation of their different redox states is carried out and their magnetic properties are investigated in the solid state by SQUID magnetometry. The expected magnetic behavior is an on/off switch of the exchange coupling between the magnetic centers depending on the presence (or absence) of unpaired electrons on the HHTP. Trinuclear complexes of nickel ions and cobalt ions are reported along with an hexanuclear nickel HHTP dimer. The study on the different isolated redox states puts in evidence the modulation of the magnetic properties with the redox switch. The observed magneto-redox switch behavior is rationalized by ab initio calculations unveiling the electronic structure of HHTP and the internal mechanisms of spin interaction. Additionally, explorations to synthesize lanthanide-based trinuclear complexes around the HHTP and binuclear complexes around the chloroanilate ligand are reported

The synthesis and characterisation of a series of {AnO₂}ⁿ⁺ complexes containing multidentate ligand environments is reported. Three novel {UO₂}²⁺ complexes (1-3) containing N₃O₂ linear pentadentate ligands have been prepared and crystallographically characterised. NMR spectroscopy has been able to show that 1-3 are stable with respect to ligand exchange, in a range of solvents. The strength of the O=U=O unit has been probed by vibrational spectroscopy and 1-3 exhibit some of the weakest O=U=O ν₁ stretching modes reported (802-805 cm⁻¹). The cyclic voltammetry (CV) of 1-3 in various solvents (0.1 M [Bu₄N][PF₆]) has been performed and indicate the position and reversibility of the {UO₂}²⁺/{UO₂}⁺ redox couple has been found to be subtly dependent on the solvation environment. {UO₂}²⁺ complexes (4-6) have been prepared by subtle modification of reaction conditions using a rigid N₂O₂S linear pentadentate ligand. Characterisation by X-Ray diffraction reveals different monometallic systems, where 4 and 5 are solely bound to the O₂ donors of the ligand and 6 exhibits uranyl binding through all of the donor atoms in the N₂O₂S cavity. ¹H NMR spectroscopy shows 5 exhibits intramolecular rearrangement on the NMR timescale in DCM, but undergoes intermolecular ligand exchange in more coordinating solvents (DMSO, py). Cyclic voltammetry of 5 in DCM (0.1 M [Bu₄N][PF₆]) also indicates that rearrangements and/or ligand exchange processes may occur at rate comparable to that of the CV studies. Complex 6 exhibits stability with respect to ligand exchange or rearrangement in various solvents and shows comparable solvation environment dependency of the {UO₂}²⁺/{UO₂}⁺ redox couple, relative to 1-3. Three monometallic {UO₂}²⁺ complexes (7-9) have been prepared using a rigid tetradentate N₂O₂ ligand. A dimetallic {UO₂}²⁺ complex (10) where two {UO₂}²⁺ are linked by a 4,4'-bipyridine bridge, has been formed by controlled ligand exchange. Vibrational spectroscopy shows the presence of the O=U=O ν₁ stretch in both the Raman and infrared spectra for 7-10, likely to be caused by distortion of the ligand about the UO₂}²⁺ equatorial plane causing a change in dipole for the O=U=O ν₁ stretching mode. A synthetic and spectroscopic study of neptunyl coordination to N₃O₂ linear pentadentate ligands has been made. Adopting a similar method that was successfully employed in the synthesis of 1-3, resulted in the reduction of {NpO₂}²⁺ to {NpO₂}⁺, giving a series of complexes (11-13). Complex 13 has been crystallographically characterised and shows a monometallic {NpO₂}⁺ complex which is bound to all of the atoms in the N₃O₂ cavity.

To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. Despite the acceleration in computer power experienced in the last decades many problems persist in modelling these complicated interactions. The main objective of this thesis was to investigate and improve molecular modelling methods aimed to estimate protein-ligand binding. In order to do so, we have utilised chemometric tools, e.g. design of experiments (DoE) and principal component analysis (PCA), in the field of molecular modelling. More specifically, molecular docking was investigated as a tool for reproduction of ligand poses in protein 3D structures and for virtual screening. Adjustable parameters in two docking software were varied using DoE and parameter settings were identified which lead to improved results. In an additional study, we explored the nature of ligand-binding cavities in proteins since they are important factors in protein-ligand interactions, especially in the prediction of the function of newly found proteins. We developed a strategy, comprising a new set of descriptors and PCA, to map proteins based on their cavity physicochemical properties. Finally, we applied our developed strategies to design a set of glycopeptides which were used to study autoimmune arthritis. A combination of docking and statistical molecular design, synthesis and biological evaluation led to new binders for two different class II MHC proteins and recognition by a panel of T-cell hybridomas. New and interesting SAR conclusions could be drawn and the results will serve as a basis for selection of peptides to include in in vivo studies.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2016.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 135-145).<br>Over the last decade, the synthesis methods of colloidal nanocrystals have advanced at an astonishing rate, producing particles that are chemically stable, monodisperse, and, in the case of semiconductor quantum dots (QDs), immensely bright. Inorganic nanocrystals linked to functional organic or biological molecules have recently emerged as a new class of nanomaterials for generating highly efficient devices, and sensing agents for a broad range of advanced applications. A key step in the synthesis of these constructs involves transforming the chemistry of the surface from that generated by the nanocrystals synthesis conditions (high boiling-point and hydrophobic solvent environment) to one possessesing the appropriate functional groups for derivatization and that is compatible with the intended final application. Here, we describe the synthesis of a series of organic ligands that modify the surface in that manner. The first ligand exhibits a norbornene functional group and binds strongly to the surface of colloidal nanocrystallites during particle synthesis, eliminating the need for ligand exchange and enabling large-scale production of high quality derivatizable nanomaterials. This ligand is compatible with state-of-the-art synthesis methods of a large variety of semiconductor nanocrystallites, including PbS, CdSe/CdS, and InAs/CdSe/CdS core/shell nanoparticles. Applications that make use of the norbornene click-chemistry functionality will be presented, along with efforts to preserve the high quantum yield and colloidal stability in water. We also introduce a bidentate carboxylate-based ligand as part of an effort to enhance the quality of QDs through the chelate effect. This ligands enhances the PLQY at high temperature, as a result of surface-related trap state passivation. Finally, we describe the synthesis of a new functional group for generating derivatizable-QDs that can be easily copolymerized with the polyimidazole ligand (PIL), and that is reactive with tetrazine and, upon thermal activation, with thiols to form stable bioconjugates.<br>by José Manuel Cordero Hernández.<br>Ph. D.

Most characterised protein-small molecule interactions that display a change in heat capacity (\bigtriangleupCp) occur with a negative \bigtriangleupCp value. This is often attributed to solvent reorganisation from reduction in solvent accessible apolar surface area accompanying complex formation. Positive \bigtriangleupCp values have not been widely reported and could typically be attributed to an increased solvent accessible apolar surface area, desolvation of polar surface area or structural transitions in the biomolecular complex. Heat shock protein-90 (Hsp90) is one of the abundant and important molecular ATP-dependent chaperones. The N-terminal domain of Hsp90 contains ATP/ADP binding site, where Hsp90-ADP interactions proceed with a large positive \bigtriangleupCp of 2.35 ± 0.46 kJ·mol-1·K-1. Interestingly geldanamycin, an Hsp90 inhibitor which binds to the same N-Hsp90-ADP/ATP binding site, interacts with a negative \bigtriangleupCp of -0.39 ± 0.04 kJ·mol-1·K-1. The semi-empirical correlation of the solvent accessible surface area change does not match well with the observed \bigtriangleupCp. This prompted us to investigate various factors affecting the thermodynamics of protein-small molecule binding including varying buffers, differing salt concentration, altering pH, substitution of different metal cations and performing interactions in heavy water. Molecular dynamics simulation and NMR studies have allowed us to disregard structural changes of N-Hsp90-ADP molecule from giving rise to positive \bigtriangleupCp. From a combination of these calorimetric, simulation and structural studies we have gathered a considerable body of evidence suggesting that the change in accessible surface area, ionic interactions and resultant desolvation of water molecules from the surface of a Mg2+ ion can contribute substantially to a positive \bigtriangleupCp. We conclude that this unique result appears to come from extensive disruption of the tightly bound water molecules present around Mg2+-ADP after binding to Hsp90, which then gives rise to a positive \bigtriangleupCp. In addition to these findings, the thermodynamics of 18 structurally related CDK2 inhibitors were investigated using ITC. CDK2 is a member of cyclin dependent kinases implicated in eukaryotic cell cycle progression and control. This investigation showed that even conservative changes in small molecule structure can reveal large variation in thermodynamic signature, while simple concepts such as van der Waals interactions, steric hindrance, and hydrophobicity are insufficient to explain it.

The central idea in Fragment Based Ligand Discovery (FBLD) is to identify small, low molecular weight compounds (MW < 250) that bind to a particular protein active site. Hits can be used to efficiently design larger compounds with the desired affinity and selectivity. Three approaches to FBLD are described in this thesis. The first topic is the development and assessment of different chemoinformatics procedures to select those fragments that maximally represent the chemical features of a larger compound library. Such a fragment library could be of great value in the so-called “SAR by Catalogue" approach, where the initial stage of fragment growth is by selecting existing compounds that contain sub-structures of the hit fragments. Five schemes implemented in the Pipeline Pilot software are described. The second project was to develop improved approaches to processing Thermal Shift Analysis (TSA) data. The shift in melting temperature can indicate that a ligand binds and thus stabilises a protein. A program, MTSA, has been written which allows more straightforward processing of the experimental data than existing available software. However, detailed analysis of fragment screening data highlighted difficulties in defining the melting temperature and suggest that TSA is not sufficiently reliable for routine screening use. Finally, a number of proteins were assessed experimentally for suitability for FBLD: N-myristoyl transferase (NMT), the bacterial homologue of a GlcNAcase enzyme (BtGH84) and the model system hen egg white lysozyme (HEWL). It was not possible to produce suitable NMT material due to the inherent instability of the protein produced in York. The screening results of HEWL with a new Surface Plasmon Resonance (SPR) assay, a cell based activity assay and TSA were inconsistent and difficult to interpret. However, BtGH84 was suitable for screening by both TSA and SPR. The resulting fragment hits are suitable starting points for further evolution.

Molecular simulations approaches are powerful tools for structural biology and drug discovery. They provide additional and complementary information on structure, dynamics and energetics of biomolecules whose structures have been determined experimentally [1,2,3,4,5,6,7]. In particular, Molecular Dynamics (MD) simulations [8], along with elastic network analysis [9], offer insights into molecular fluctuations, conformational changes and allosteric mechanisms. In addition, molecular simulation can be used to design novel and potent ligands to a specific target (either a protein or DNA) as well as to estimate ligands potency [10,11]. Attempts at predicting protein structures using bioinformatics and MD are also increasingly successful [12,13,14,15], as well as approaches that use solely simulation tools [16]. The development of new algorithms and the continuously growing computer power currently allow for the simulation of more and more complex biological systems, such as protein aggregates [7,17,18,19,20] and protein/DNA complexes [21]. In this context, a number of theoretical techniques (namely molecular dynamics simulations, elastic network analysis, electrostatic modeling and binding energy predictions) have here been applied to the study of specific proteins. On the basis of X-ray protein structures, molecular simulations have provided a detailed description of internal motions and interactions, which are not evident from the experimental data and have functional implications. First, we have used MD to investigate structural features, focusing on the differences between the solid state and the aqueous solution structures. Over 80% of data in the PDB [22] are X-ray structures, making protein crystallography the major resource in structural biology. Nevertheless, in a few cases, the structural details might be affected by environmental features, such as the presence of small compounds in the buffering solution and/or crystal packing contacts due to the periodic lattice. Here, a comparative MD study has been performed on the Catabolite Activator Protein (CAP), in both the crystal phase and in the aqueous solution. CAP is a bacterial DNA-binding transcription regulator whose activity is controlled by the binding of the intracellular mediator cyclic Adenosine MonoPhosphate (cAMP). CAP is a homodimeric protein and each subunit is formed by a cyclic nucleotide- and a DNA-binding domain. Inspection of the available CAP X-ray structure within the crystal environment [23] suggests that packing contacts do affect the native conformation of the ligand activated protein. Anticipating our results, we have found that indeed the conformation of the protein in solution is different, and that these differences may play a role for CAP biological function. Next, we have used molecular simulations to target structural flexibility. Conformational fluctuations often play a key role for the protein function and MD simulations can provide information on large-scale concerted motions of proteins [24,25,26]. We have addressed this point in the context of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) cation channel. The tetrameric HCN channels are opened by membrane hyperpolarization, while their activation is allosterically modulated by the binding of cAMP in the cytoplasm. The cytoplasmic part of the HCN2 channel, which is responsible for the channel modulation, has been here investigated by MD simulations and elastic network analysis, on the basis of the available X-ray structure [27], to earn new insights into the molecular mechanism triggered by cAMP. We have found that, in the presence of cAMP, the protein undergoes a quaternary structure oscillation, in which each subunit moves as a rigid body. This fluctuation, which is not observed in the absence of cAMP, could facilitate the channel opening transition. Finally, we have moved our attention to an issue relevant for structure-based drug design. Within a long-standing collaboration with Prof. Cattaneo’s lab (SISSA and Motivations and Summary 7 Layline Genomics), our group has been interested in the design of mimics of proteins involved in the biochemical pathways that lead to the Alzheimer’s disease. Here, on the basis of structural information [28], we have designed a peptide that could specifically target trkA, the high affinity receptor of the Nerve Growth Factor (NGF), which is a protein that plays a critical role for the development, survival and maintenance of neurons in the vertebrate nervous system and activates signaling pathways related to neuroprotection. The results of this research will be tested at the Prof. Cattaneo’s Lab in order to validate the theoretical findings and assess the potency and the effects of such a ligand.

Ligand design in general enables the formation of coordination compounds with multiple functionalities within a single framework. To date, two of the most widely studied ligands are 2,2′:6′,2′′-terpyridine (terpy) and acetylacetone (acac), whose tridentate and bidentate coordination pockets, respectively, enables the formation of metallic complexes with various geometries. The Brusso group had been incorporating imidoyl amidine (ImAm) ligands to build different materials such as organic radicals and fluorescent materials. In particular, the ligands N-2-pyridylimidoyl-2-pyridylamidine (Py2ImAm) and N-2-pyrimidylimidoyl-2-pyrimidylamidine (Pm2ImAm) were recently synthesized and have great appeal to build metallic complexes, as they poses two coordination sites similar to those in terpy and acac. The work presented herein represents the first studies involving the coordination of Py2ImAm and Pm2ImAm as discrete ligands. Our results demonstrate the versatility of these ligand frameworks, in which discrete mononuclear complexes, homometallic and heterometallic polynuclear complexes may be realized. Chapter one serves as a brief introduction to transition metal chemistry and has a comprehensive review of the coordination chemistry of the ImAm ligand framework. In chapter two, the selective coordination of first row transition metals into the bidentate or tridentate sites of Py2ImAm is explored. The formation of these mononuclear complexes is acid-base driven, where a weak acid induces coordination to the tridentate site and a weak base leads to coordination in the bidentate site. Coordination to both sides of Pm2ImAm with manganese or iron is explored in chapter three. The results show the formation of unusual tetranuclear complexes with the metal ions in both low spin and high spin configurations. Chapter four covers the coordination to cobalt, and the formation of polynuclear complexes with different geometries using Pm2ImAm. The magnetochemistry of these cobalt polynuclear complexes is also presented and reveal a single molecule magnet behaviour for one of the complexes. Finally, in chapter five, a one-pot synthesis of copper-manganese heterometallic complexes is presented. Overall, these imidoyl amidine ligands are able to build complexes with different geometries, different electronic configurations (i.e. low or high spin), and different metal ions. These results show a great versatility of ImAm ligands and suggest the future use of these ligands by other research groups.

Nous proposons un ensemble de méthodes pour la conception de systèmes moléculaires. Notre stratégie consiste à utiliser comme modèle des machines naturellement optimisées, les protéines. Les protéines peuvent être des briques structurales, des transporteurs d'informations ou des catalyseurs chimiques. Nous utilisons ici des approches computationnelles, complémentaires aux voies expérimentales, pour concevoir de tels systèmes.Nous avons d'abord entièrement redessiné un domaine PDZ impliqué dans des voies métaboliques. Nous utilisons une approche physics-based basée sur la mécanique moléculaire, un modèle de solvant implicite et un échantillonnage Monte Carlo. Parmi plusieurs milliers de variants prédits pour adopter le repliement PDZ, trois ont été sélectionnés et montrent un repliement correct. Deux ont une affinité détectable pour les ligands peptidiques naturels.Nous avons ensuite re-dessiné le site actif de l'enzyme méthionyl-ARNt synthétase (MetRS). En utilisant un algorithme de type Monte Carlo adaptatif, nous avons sélectionné des variants pour l'affinité MetRS/méthionine (Met). Sur 17 variants testés expérimentalement, 17 sont actifs. La méthode a été ensuite appliquée à l'état de transition pour sélectionner des variants directement sur leur efficacité catalytique.Nous avons étudié la possibilité de modifier la MetRS pour étendre son activitéaux acides aminés β, afin d'étendre le code génétique. Ces acides aminésnon-naturels permettraient d'enrichir le répertoire structural des protéines. 20variants MetRS obtenus à partir de prédictions d'affinité MetRS/β-Met ont ététestés. Aucun n'augmente l'activité mais trois ont amélioré la sélectivité enfaveur de la β-Met. Nous avons implémenté une méthode de sélection de positionsd'intérêt et production de variants pour β-Met et β-Val. Une vingtaine deprédictions sont en cours de tests expérimentaux.Enfin, la modification de protéines in vivo pose la question de leur dérive génétique. Nous introduisons ici une méthode de conception de paires de gènes chevauchants pour des domaines PDZ. Ce codage permettrait de limiter la dérive génétique. Nous avons produit près de 2000 paires de domaines PDZ au codage chevauchant, dont une a été validées par 2 microsecondes de dynamique moléculaire. Des tests expérimentaux sont en cours<br>We propose a set of methods to design molecular systems. We start from naturally optimized components, namely proteins. Proteins can act as structural components, information transporters, or catalysts. We use computational methods to complement experiments and design protein systems.First, we fully redesigned a PDZ domain involved in metabolic pathways. We used a physics-based approach combining molecular mechanics, continuum electrostatics, and Monte Carlo sampling. Thousands of variants predicted to adopt the PDZ fold were selected. Three were validated experimentally. Two showed binding of the natural peptide ligand.Next, we redesigned the active site of the methionyl-tRNA synthetase enzyme (MetRS). We used an adaptive Monte Carlo method to select variants for methionine (Met) binding. Out of 17 predicted variants that were tested experimentally, 17 were found to be active. We extended the method to transition state binding to select mutants directly according to their catalytic power.We redesigned the MetRS binding site to obtain activity towards two β-amino acids, in order to expand the genetic code. These unnatural amino acids can enhance the structural repertoire of proteins. 20 predicted mutants were tested. Although none had increased β-Met activity, three had a gain in selectivity for β-Met. We then implemented a method to select optimal positions for design and applied it to β-Met and β-Val. Around 20 variants are being experimental tested.Finally, in vivo protein modifications raise the question of their eventual drift away from the original design. We introduce here a design approach for overlapping genes coding PDZ domains. This overlap would reduce genetic drift and provide bio-confinement. We computationally produced almost 2000 pairs of overlapping PDZ domains. One was validated by 2 microsecond molecular dynamic simulations. Experiments are underway