Molecular Nanomagnets have been proposed as plausible candidates in a variety of futuristic applications. Thorough understanding of the magnetic properties of these systems is therefore necessary to develop devices that include such units. The aim of this thesis is to synthesise and structurally and magnetically characterise a range of systems that could be used as elementary units in three proposed applications such as: data storage devices, magnetic refrigerants and qubits for quantum computing. A series of mixed 3d/4f metal complexes were synthesised through solvothermal reactions and characterised by X-ray single crystal diffraction and SQUID magnetometry. Through indirect methods it was possible to obtain high magnetic entropy change for some systems. It was also possible to obtain some insight into the magnetic interactions within the systems through modelling the magnetic data. The role of the 4f-4f and 3d-4f interactions in two sets of molecules is also described. The first study is in an asymmetric dysprosium dimer, where through a range of experimental techniques and advanced theoretical methods, such ab-initio calculations we are able to explain the role of the intramolecular interactions and their effect on the SMM properties of this system. Similarly, insight into the role of the 3d-4f interactions is achieved through the observation of the magnetic behaviour of a family of 27 tetranuclear systems, though SQUID data and ab-initio calculations. Finally, chemical functionalization of a well-proposed qubits, namely {Cr7Ni} and subsequent reaction with a redox active metal ion, CoII/III, two {Cr7Ni} systems are linked. The magnitude of the exchange interaction between the {Cr7Ni}-CoII-{Cr7Ni} was determined through Electron Paramagnetic Resonance. Furthermore, by chemical oxidation/reduction of the cobalt between paramagnetic and diamagneticstates, i.e. CoII and CoIII respectively, we demonstrate that the interaction can be switched ON/OFF. This characteristic makes of these systems candidates to function as a SWAP gate.

The introductory Chapter to this thesis outlines fundamental aspects of 4f lanthanide(III) coordination chemistry, in particular compounds that possess the intriguing properties of slow relaxation of magnetisation, (or the ability to behave as single-molecule magnets, SMMs). The recent renaissance into the study of the magnetic behaviour of 4f-coordination complexes has led to the consideration of utilising organometallic precursors for the development of novel lanthanide containing compounds, which may possess interesting magnetic properties, subsequently forming the basis of Chapter Two. In Chapter Two, the syntheses and structures of the novel lithiated thiolate ligand, lithium triphenylsilylthiolate, (Ph3SiS-Li) (2.1), and the sulfur-bridged, dimetallic dysprosium(III) and gadolinium(III) complexes [(MeCp)2Dy(µ-SSiPh3)]2 (2.2) and [(MeCp)2Gd(µ-SSiPh3)]2 (2.3), are described in detail. The structural and physical properties of these compounds are analysed through NMR, elemental analysis and SQUID magnetometry, alongside supporting theoretical calculations to reveal that compound 2.2 is the first dimetallic, sulfur-bridged SMM reported, giving an energy barrier to the reversal of magnetisation of Ueff = 192 ± 5 K.56bChapter Three reports on the structural development of a series of lanthanide monomers, exhibiting the general motif [Ln(OSiPh3)3(THF)3] (where Ln = Dy(3.4), Er(3.5), Ho(3.6), Gd(3.7), Tb(3.8)), exploiting the siloxide ligand Ph3SiOH through two novel synthetic routes. This Chapter also provides new analytical insight to these complexes by exploring their magnetic properties through a series of SQUID measurements and through the analysis of their electronic properties using air sensitive, variable temperature optical absorption spectroscopy. Compounds 3.4 and 3.5 were revealed to be SMMs, with 3.5 having a much higher thermal barrier to the reversal of magnetisation, Ueff = ~ 28 K, than 3.4, which are supported by theoretical analysis. Chapter Four describes the utility of ligand 2.1 and Ph3SiOH in the context of 3d transition metal cyclopentadienyl chemistry, outlining the syntheses and structures of three distinct compounds; the trimetallic, [Cp2Mn3(µ-OSiPh3)4](4.7), the hetero-cubane tetramer [CpMn(µ-SSiPh3)]4 (4.8) and the dimetallic thiolate-bridged [CpCr(µ-SSiPh3)]2 (4.9) compound. These compounds were formed in reactions exploiting organometallic manganocene and chromocene precursors. Magnetic susceptibility measurements were conducted on these compounds to gain further insight into their structural properties. The magnetic exchange coupling constants for Mn(II) compounds 4.7 and 4.8 were J = - 4.4 cm-1 and J = - 3.0 cm-1 respectively. Furthermore, having demonstrated the use of metal-cyclopentadienyl building blocks in the synthesis of novel SMMs, Chapter Five discusses the possibility of further advancement on the development of this class of magnetic molecules.

abstract: The cell is a dense environment composes of proteins, nucleic acids, as well as other small molecules, which are constantly bombarding each other and interacting. These interactions and the diffusive motions are driven by internal thermal fluctuations. Upon collision, molecules can interact and form complexes. It is of interest to learn kinetic parameters such as reaction rates of one molecule converting to different species or two molecules colliding and form a new species as well as to learn diffusion coefficients. Several experimental measurements can probe diffusion coefficients at the single-molecule and bulk level. The target of this thesis is on single-molecule methods, which can assess diffusion coefficients at the individual molecular level. For instance, super resolution methods like stochastic optical reconstruction microscopy (STORM) and photo activated localization microscopy (PALM), have a high spatial resolution with the cost of lower temporal resolution. Also, there is a different group of methods, such as MINFLUX, multi-detector tracking, which can track a single molecule with high spatio-temporal resolution. The problem with these methods is that they are only applicable to very diluted samples since they need to ensure existence of a single molecule in the region of interest (ROI). In this thesis, the goal is to have the best of both worlds by achieving high spatio-temporal resolutions without being limited to a few molecules. To do so, one needs to refocus on fluorescence correlation spectroscopy (FCS) as a method that applies to both in vivo and in vitro systems with a high temporal resolution and relies on multiple molecules traversing a confocal volume for an extended period of time. The difficulty here is that the interpretation of the signal leads to different estimates for the kinetic parameters such as diffusion coefficients based on a different number of molecules we consider in the model. It is for this reason that the focus of this thesis is now on using Bayesian nonparametrics (BNPs) as a way to solve this model selection problem and extract kinetic parameters such as diffusion coefficients at the single-molecule level from a few photons, and thus with the highest temporal resolution as possible. / Dissertation/Thesis / Source code related to chapter 3 / Source code related to chapter 4 / Doctoral Dissertation Physics 2020

Spatial and temporal dynamics of polymer chains play critical roles in their rheological properties, which have a significant influence on polymer processing and fabrication of polymer-based (nano) materials. Many theoretical and experimental studies have aimed at understanding polymer dynamics at the molecular level that give rise to its bulk phase properties. While much progress has been made in the field over the past ~60 years, many aspects of polymers are still not understood, especially in complicated systems such as entangled fluids and polymers of different topologies. In addition, the physical properties of biological macromolecules, i.e. DNA, are expected to affect the spatial organization of chromosome in a cell, which has the potential impact on a broad epigenetics research. Here, we propose new methods for simultaneous visualization of diffusive motion and conformational dynamics of individual polymer chains, two most important factors that characterize polymer dynamics, based on a new single-molecule tracking technique, cumulative-area (CA) tracking method. We demonstrate the applicability of the CA tracking to the quantitative characterization of the motion and relaxation of individual topological polymer molecules under entangled conditions, which is possible only by using the newly-developed CA tracking, using fluorescently-labeled linear and cyclic dsDNA as model systems. We further extend the technique to multi-color CA tracking that allows for the direct visualization and characterization of motion and conformation of interacting molecules. We also develop a new imaging method based on recently developed 3D super-resolution fluorescence microscopy technique, which allows direct visualization of nanoscale motion and conformation of the single molecules that is not possible by any other methods. Using these techniques, we investigate spatial and temporal dynamics of polymers at the single-molecule level, with special emphasis on the effect of topological forms of the molecules and the confined geometry on their spatiotemporal dynamics. Our results demonstrate that the new methods developed in this thesis provide an experimental platform to address key questions in the entangled topological polymer dynamics. The research will provide a platform for developing new polymer-based materials and open the possibility of studying spatial organization of DNA in a confined geometry from physics point of view.

In order to monitor the T7 replisome fate upon encountering abasic lesion, I optimized a single molecule flow stretching assay where the replisome encounters either abasic site or undamaged site inserted at 3.5 kilobases from the replication fork. The obtained events were categorized into three groups; bypass, restart and permanent stop. The results showed 52% bypass, 39% pause and 9% stop upon encountering the abasic lesion. The pause duration in the restart events was found to be ten times longer than the undamaged one. Moreover, an ensemble experiment was performed, and the results were slightly consistent with regard to the bypass percentage (70%) but the stoppage percentage was significantly higher in the ensemble replication reaction (30%). Further investigations were made and it was found that the rate of the T7 replisome increases after bypassing the abasic lesion. To inquire more about this rate switch and the difference between the single molecule and ensemble results, another unwinding experiment was performed where only gp4 (helicase) was used from the replisome. Interestingly, the rate of DNA unwinding by gp4 was similar to the rate observed after the replisome bypasses the lesion. We hypothesize that the polymerase is stalled at the abasic site and its interaction with the helicase is lost. Consequently, the helicase and the polymerase will uncouple where the helicase continues unwinding the DNA to result in a higher observed rate after bypassing the abasic site. Additional studies will be performed in the future to directly observe the helicase and polymerase uncoupling upon encountering the lesion.

No description available.

Les molécules-aimants sont des complexes moléculaires contenant des ions des métaux de transition ou des lanthanides capables de présenter le phénomène de blocage de l’aimantation en dessous d’une température de blocage Tb. Ce blocage est dû à la présence d’une barrière d’énergie de réorientation de leur aimantation à cause de la présence d’une anisotropie magnétique uniaxiale qui conduit à la présence de deux états stables de l’aimantation.Ces deux états stables sont adressables avec un champ magnétique extérieur. Il est donc,théoriquement, envisageable d’utiliser ces molécules comme unités de base pour le stockage « classique » de l’information.Néanmoins, à cause de la nature quantique des molécules, une relaxation entre les deux états de l’aimantation a lieu à basse température par effet tunnel à travers la barrière d’énergie. Cet effet tunnel a plusieurs causes dont une correspondant à une légère déviation de l’anisotropie magnétique de la situation strictement axiale. Cet effet annule le caractère bistable (classique) des molécules les rendant inutilisables comme bits classiques pour le stockage de l’information. Mais, la présence de l’effet tunnel conduit à une situation particulière à basse température où deux niveaux sont présents séparés par une énergie liée au caractère non axiale (rhombique) de l’aimantation (cas où le spin est entier). Un système à deux niveaux est appelé bit quantique(qubit) et constitue l’unité de base pour la construction d’ordinateurs quantiques si plusieurs conditions sont réunies.Ainsi, pour concevoir des bits classiques ou quantiques, il est indispensable comprendre au niveau microscopique la nature de l’anisotropie magnétique et les facteurs qui l’influencent.Ce travail de thèse est consacré à l’étude théorique de la nature de l’anisotropie magnétique dans des complexes mononucléaires et binucléaires de Ni(II) (S = 1)et de Co(II) (S = 3/2). Des calculs de type ab initio, basés sur la théorie de la fonction d’onde,qui permettent d’extraire les paramètres de l’hamiltonien de spin de l’anisotropie magnétique ont été effectués. Des calculs sur des objets modèles et molécules réelles qui permettent de séparer l’effet des différents paramètres structuraux et électroniques des ligands sur la nature et l’amplitude de l’anisotropie magnétique ont aussi été réalisés.La comparaison entre les calculs sur des complexes modèles et sur des complexes réels permet de rationaliser les propriétés magnétiques des complexes réels et surtout de proposer des stratégies pour la synthèse de nouveaux complexes avec les propriétés souhaitées. L’étude de complexes binucléaires qui peuvent être considérés comme la première étape pour la conception de porte logique quantique a été réalisée. Les calculs sur les complexes binucléaires sont réalisés en fragmentant les molécules en deux espèces mononucléaires. Pour les complexes binucléaires de Ni(II) et Co(II), des calculs de type Density Functional Theory (DFT) pour évaluer l’amplitude et la nature de l’interaction d’échange ont été menés. Pour étudier l’influence d’une perturbation extérieure sur les propriétés magnétiques, l’influence d’un champ électrique placé parallèle et perpendiculaire à l’axe de facile aimantation d’un complexe de Ni(II) a été étudiée. Le champ électrique peut influencer les propriétés d’anisotropie de manière importante ouvrant la possibilité à la manipulation des molécules par cette perturbation. / Single molecule magnets are molecular complexes containing transition metal or lanthanides ions which are able to block their magnetization below a certain blocking temperature Tb. This blocking is caused by an energy barrier separating the two orientations of magnetization leading to two stable magnetization states. These two states can be controlled by an external magnetic field.Therefore, it is theoretically possible to use these molecules as bits which are able to store“classical” information. However, due to the quantum nature of these molecules, the relaxation of magnetization can exist even at low temperatures. This phenomenon is called the quantum tunneling effect and prevents the bistable (classical) behavior of the magnetic properties, as well as their use as classical bits for data strorage.Yet, the quantum tunneling of the magnetization also leads to a particular situation at a low temperature where two levels are separated by an energy related to the non-axial character(rhombic) of the magnetization (when the spinis an integer). Such two-levels system could be used as a quantum bit (qbit) which is the basic unit for quantum information processing. Thus,the design of classical or quantum bits require a precise understanding of magnetic properties and their origin at a microscopic level.The Ph.D work was devoted to the theoretical study of the magnetic anisotropy in mononuclear and binuclear Ni(II) (S=1) and Co(II) (S=3/2) complexes. Ab initio calculations based on the wave function theory were carried out and the spin Hamiltonian parameters were extracted. Model complexes were used to investigate the structural and electronic parameters causing magnetic anisotropy.Calculations were, also, performed on complexes synthesized in the laboratory.Comparison between real and model complexes allowed rationalizing the magnetic properties and imagining new synthesis strategies leading to the desired magnetic properties. Binuclear complexes that can be considered as double qbits and used to build quantum logic gates were also investigated. The calculations were performed by fragmenting the binuclear complexes into two mononuclear units in order to study the local anisotropy of each metal ion.The exchange interaction was investigated using Density Functional theory (DFT). In order to study the influence of an external perturbation on magnetic properties, the magnetic properties of a mononuclear Co(II) complex under an external electric field applied parallel or perpendicular to the axis of easy magnetization were calculated. The application of an electric field can lead to important modifications of magnetic properties. Thereby, offering the possibility to the manipulation of these molecules by external electric fields.

The controlled assembly of molecular building blocks is an emerging strategy that allows for the preparation of materials with tailor-made properties. This involves the precise combination of molecular subunits that interact with one another via specifically designed reactive sites. Such a strategy has produced materials exhibiting remarkable properties, including those based on metal-organic frameworks and single-molecule magnets. The present Thesis aims to highlight how such metal-organic assemblies can be engineered at the molecular level to promote certain desired functionalities. Specifically, Chapter 2 will focus on the confinement effects of a crystalline sponge on a ferrocene-based guest molecule that is nanostructured within the porous cavities of a host material. In doing so, we evaluate how one can exert some level of control over the binding sites of the guest molecule, through the addition of electron-withdrawing groups, as well as tuning the physical properties of the guest itself through molecular encapsulation. Notably, we demonstrate a distinct change in the dynamic rotational motion of the ferrocene molecules once confined within the crystalline sponge. In Chapter 3, we investigate the generation of slow relaxation of the magnetization from a Co(II)-based metal-organic framework. We compare this to a closely related 2D Co(II) sheet network, and how slight changes in the crystal field, probed through computational methods, can impact the magnetic behaviour. This type of study may be particularly beneficial in the optimization of single-ion magnets, by sequestering metal centres in select chemical environments, and minimizing molecular vibrations that may offer alternative magnetic relaxation pathways. We extend these principles in Chapter 4, through the use of a nitrogen-rich ligand that acts as a scaffold for Ln(III) ions, thereby yielding 0D and 1D architectures. The coordination chemistry of Ln(III) ions with N-donor ligands remains scarce, especially when evaluated from a magnetic perspective, and therefore, we sought to determine the magnetic behaviour of such compounds. The monomeric unit displays clear single-molecule magnet behaviour with an energetic barrier for the reversal of the magnetization, while the 1D chain displays weaker magnetic characteristics. Nevertheless, such compounds incorporating nitrogen-rich ligands offer much promise in the design of environmentally-friendly energetic materials. In Chapter 5, we take a look at different two different systems that involve the formation of radical species. On one hand, we can promote enhanced magnetic communication between Ln(III) ions, which is typically quite challenging to achieve given the buried nature of the 4f orbitals, and on the other hand, we rely on a redox-active ligand to design stimuli-responsive metal-organic assemblies. The latter case provides access to “smart” molecular materials that can respond to changes in their environment. Here, a multi-stimuli responsive nanobarrel was studied, which displayed sensitivity to ultraviolet radiation, heat and chemical reduction. Lastly, Chapter 6 provides a new method for the systematic generation of cationic frameworks, termed Asymmetric Ligand Exchange (ALE). This strategy focuses on the replacement of linear dicarboxylates with asymmetric linkers that features one less negative charge, in order to tune the ionicity of porous frameworks. This allows for the retention of the structural topology and chemical reactivity of the original framework, representing distinct advantages over other similar strategies. Methods to retain permanent porosity in such cationic frameworks are also proposed. Altogether, these studies highlight how the directed assembly of ordered networks can generate varied properties of high scientific interest.

I develop an analytically tractable model of dynamic force spectroscopy by considering the forced escape of a Brownian particle out of a potential well, along a one-dimensional reaction pathway. I compute explicit expressions for pertinent experimental observables, such as average bond lifetimes and rupture force distributions. The results generalize conventional quasistatic theories to arbitrary forces and loading rates, thus covering the whole range of conditions found in experiments and all-atom simulations. The theory is extended to so-called catch-slip bonds that play an important role in biology, and to “hidden” degrees of freedom, which may bear significantly on the observed bond kinetics at high loading rates.

Cytoplasmic dynein is a ubiquitous minus-end directed motor protein that is essential for a variety of cellular processes ranging from cargo transport to spindle and chromosome positioning. Specifically, in fission yeast during meiotic prophase, the fused nucleus follows the spindle pole body in oscillatory movements from one cell pole to the other. The three molecular players that are essential to this process are: (i) the motor protein dynein, which powers the movement of the nucleus, (ii) microtubules, which provide the tracts for the movement and (iii) Num1, the anchor protein of dynein at the cortex. Dyneins that are localized to the anchor protein at the cortex and simultaneously bound to the microtubule emanating from the spindle pole body, pull on that microtubule leading to the movement of the nucleus. The spindle pole body, by virtue of its movement establishes a leading and a trailing side. Previous work by Vogel et al. has elucidated the mechanism of these oscillations as that of asymmetric distribution of dynein between the leading and trailing sides. This differential distribution is a result of the load-dependent detachment of dynein preferentially from the trailing microtubules. This self-organization model for dynein, however, requires a continuous redistribution of dynein from the trailing to the leading side. In addition, dyneins need to be bound to the anchor protein to be able to produce force on the microtubules. Anchored dyneins are responsible for many other important processes in the cell such as spindle alignment and orientation, spindle separation and rotation. So we set out to elucidate the mechanism of redistribution of dynein as well as the targeting mechanism of dynein from the cytoplasm to cortical anchoring sites where they can produce pulling force on microtubules. By employing single-molecule observation using highly inclined laminated optical sheet (HILO) microscopy and tracking of fluorescently-tagged dyneins using a custom software, we were able to show that dyneins redistributed in the cytoplasm of fission yeast by simple diffusion. We also observed that dynein bound first to the microtubule and not directly to the anchor protein Num1. In addition, we were able to capture unbinding events of single dyneins from the microtubule to the cytoplasm. Surprisingly, dynein bound to the microtubule exhibited diffusive behaviour. The switch from diffusive to directed movement required to power nuclear oscillations occurred when dynein bound to its cortical anchor Num1. In summary, dynein employs a two-step targeting mechanism from the cytoplasm to the cortical anchoring sites, with the attachment to the microtubule acting as the intermediate step.