Coordination chemistry

A coordination complex is a chemical compound consisting of a central atom or ion, which is usually metallic and is called the coordination centre, and a surrounding array of bound molecules or ions, that are in turn known as ligands or complexing agents. Many metal-containing compounds, especially those that include transition metals (elements like titanium that belong to the periodic table's d-block), are coordination complexes. Coordination complexes are so pervasive that their structures and reactions are described in many ways, sometimes confusingly. The atom within a ligand that is bonded to the central metal atom or ion is called the donor atom. In a typical complex, a metal ion is bonded to several donor atoms, which can be the same or different. A polydentate (multiple bonded) ligand is a molecule or ion that bonds to the central atom through several of the ligand's atoms; ligands with 2, 3, 4 or even 6 bonds to the central atom are common. These complexes are called chelate complexes; the formation of such complexes is called chelation, complexation, and coordination. The central atom or ion, together with all ligands, comprise the coordination sphere. The central atoms or ion and the donor atoms comprise the first coordination sphere. Coordination refers to the "coordinate covalent bonds" (dipolar bonds) between the ligands and the central atom. Originally, a complex implied a reversible association of molecules, atoms, or ions through such weak chemical bonds. As applied to coordination chemistry, this meaning has evolved. Some metal complexes are formed virtually irreversibly and many are bound together by bonds that are quite strong. The number of donor atoms attached to the central atom or ion is called the coordination number. The most common coordination numbers are 2, 4, and especially 6. A hydrated ion is one kind of a complex ion (or simply a complex), a species formed between a central metal ion and one or more surrounding ligands, molecules or ions that contain at least one lone pair of electrons.

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Summary

Preparation and Analysis of Bacteria Surface-Modified with Polymer Nanoparticles

Lisa Patricia Elisabeth Bader

Cell-based drug carriers present an interesting approach to improve the targeted delivery of therapeutic drugs in vivo. Specifically, bacterial cells possess interesting properties such as motility and sensing that allow some strains to selectively target tumor areas. Immobilization of abiotic materials on the cell surface of such bacterial cells can therefore enable the delivery of therapeutic compounds at the desired location. The work presented in this thesis explores the fabrication and characterization of bacteria-nanoparticle biohybrids as potential carriers for drug delivery applications.Chapter 1 presents a review of the scientific literature that covers the different approaches to immobilize abiotic materials on the surface of bacteria. It highlights the advantages of using cells as carriers for the transport of therapeutics. An effective drug delivery agent should present great motility, viability, biodistribution and biocompatibility with human cells. Examples of various chemical approaches to surface-modify bacteria are presented. Chapter 2 systematically explores the immobilization of polystyrene nanoparticles on the surface of Escherichia coli (E. coli) and Salmonella typhimurium (Salmonella) cells. We compared the nanoparticle immobilization using four different conjugations strategies (electrostatic, covalent and ligand-ligand) and characterized the bio-hybrids systems using flow cytometry and confocal microscopy. Two different microscopy techniques were used: the first was based on 3D-reconstruction of z-stacks of single bacterium to investigate position of nanoparticles on the membrane; the second allowed for a large screening of bacteria followed by image processing determining the area of bacteria covered by nanoparticles. We observed that the efficiency of the surface modification is correlated to the initial nanoparticle/cell ratio and that non-covalent strategies allowed for increased number of biohybrids formed and nanoparticle attached. This study provides an overview of the variety of conjugation strategies (and their conjugation efficiencies) available for fabricating nanoparticle-decorated bacteria and presents us an opportunity to better understand and design bacteria-based target-specific drug delivery systems.Chapter 3 presents the characterization of the previously developed bacteria-nanoparticle biohybrids as potential carriers for nanoparticle transport. The viability of the various conjugates was determined by flow cytometry indicating a decrease in cell viability with increasing numbers of nanoparticles immobilized on the membrane. The motility was studied to investigate the impact of nanoparticle attachment on the bacterial velocity as well as the capacity to transport the cargo. Bacteria were able to transport nanoparticles when prepared with low ratios of nanoparticle/cell.

EPFL2022

Low-energy Electron Holography Microscope for Imaging of Single Molecules

Sven Alexander Szilagyi

Structure determination techniques are an essential tool to investigate and understand molecules, especially in biology, where functionality crucially depends on structure. The dominant high-resolution methods, such as transmission electron microscopy and X-ray diffraction, rely on ensemble averaging, making them unsuitable for evidencing structural variations of flexible molecules. Common single-molecule imaging techniques like scanning probe microscopy achieve high resolution but lack access to 3D objects. A possible way to overcome these limitations is offered by low-energy electron holography (LEEH). So far, LEEH achieved molecular imaging at resolutions in the range of 7-8 Å on the single-molecule level. A resolution in the range of a few Å, which would give access to atomic details of molecular structures, is in theory attainable. Obtaining a resolution near the theoretical limit requires a fully optimized LEEH setup and workflow, for which in particular sample and emitter preparation are crucial. Here, I present a novel LEEH microscope with a unique experimental workflow, which is capable of resolving molecular substructures with an unprecedented resolution for LEEH experiments. The newly constructed LEEH microscope takes advantage of an efficient vibration isolation system and is remote-controlled to minimize external perturbations. The setup is capable of low-temperature (50 K) measurements, which enhances the stability of the system. A reliable way for preparing highly coherent electron emitters constituted by sharp tungsten tips is presented along with different methods for improving their performance via functionalization and UHV treatments. I show an optimized and reliable substrate preparation protocol resulting in ultra-clean free-standing single-layer graphene (SLG) samples. Native electrospray ion beam deposition (ES-IBD) allows for the transfer of non-volatile molecules from solution into gas phase and onto the substrate. By employing a quadrupole mass selection, highly pure molecular ion beams are obtained, which are soft-landed onto the SLG substrate in a controlled and reproducible manner while retaining an intact structure. This versatile preparation method allows us to study a great variety of molecules by LEEH. Data on proteins with masses ranging from 12-820 kDa reveal molecular shapes consistent with model structures. Locally, structural details as small as 5 Å were identified, thus we are approaching our goal of a resolution in the range of a few Å. The application of our methodology to flexible proteins, exemplified by antibodies, allowed for the imaging of their conformational variability and for determining the influence of the sample preparation on their structure. This gave us the possibility to directly image gas-phase related conformations. Data of compact molecular systems with masses below 3 kDa reveal that our LEEH microscope is able to investigate small molecules, such as porphyrines, at high imaging contrast. The presented results indicate that an optimized LEEH setup and workflow in combination with ES-IBD is a versatile microscopy method, which is filling the gap between high-resolution and single-molecule techniques by elucidating structural details of various molecular species.

EPFL2022

Drops: Controlled crystallization of organic crystals and their use as matrix materials for encapsulation of volatiles

Aysu Ceren Okur

Encapsulation techniques open up new possibilities to control the kinetics and location of the release of active ingredients. Despite the progresses achieved to obtain a better control over the dimensions and composition of the capsules, the encapsulation of volatile substances is still challenging, even though it is of high relevance especially for the cosmetic industries. One way of encapsulating volatile substances is by kinetically arresting these molecules in a matrix which has a low permeability. A group of materials that likely is well-suited to generate such matrices is composed of small molecules capable of forming crystals.In this thesis, we will investigate the influence of the processing of composites containing small biocompatible organic molecules that serve as matrices with volatile active ingredients on the structure and permeability of the resulting particles. In particular, we will investigate the possibility to use organic salt crystals as matrix materials. Particles of well-defined sizes and compositions will be produced in double emulsions where the influence of the formation kinetics and confinements on the structure and permeability of the particles will be investigated. In addition, we will produce amorphous particles by kinetically suppressing the crystallization reaction using a microfluidic spray-drier. This will be achieved by co-spray-drying the active ingredient with the matrix material. We will investigate the effect of the drying speed and reactant composition on the structure and composition of the resulting particles and relate that to the release kinetics of the active ingredient. In addition, we will crystallize the amorphous composite particles and investigate the influence of the structure on the distribution of the actives within the matrix and its permeability. This project is done in collaboration with Firmenich who has all the infrastructure to quantify the release kinetics of volatile active ingredients.

EPFL2022

Crystal Field Theory: Spectrochemical Series CH-222: Coordination chemistry

Explores the Spectrochemical Series for metals and ligands, Crystal Field Splitting, Jahn-Teller distortion, and bonding interactions in coordination compounds.

Coordination Chemistry: Ligands and Geometries CH-222: Coordination chemistry

Covers coordination numbers, common ligands, and preferred geometries in coordination chemistry, emphasizing the spatial distribution between ligands and the role of d⁸ electron configurations.

Chemical Bonding: Lewis Structures and Molecular Shapes CH-160(en): Advanced general chemistry (english)

Explores chemical bonding, Lewis structures, molecular shapes, and molecular polarity.

Chemical substances

A chemical substance is a form of matter having constant chemical composition and characteristic properties. Chemical substances can be simple substances (substances consisting of a single chemical element), chemical compounds, or alloys. Chemical substances that cannot be separated into their simpler constituent elements by physical means are said to be 'pure'; this notion intended to set them apart from mixtures.

Organometallic chemistry

Organometallic chemistry is the study of organometallic compounds, chemical compounds containing at least one chemical bond between a carbon atom of an organic molecule and a metal, including alkali, alkaline earth, and transition metals, and sometimes broadened to include metalloids like boron, silicon, and selenium, as well. Aside from bonds to organyl fragments or molecules, bonds to 'inorganic' carbon, like carbon monoxide (metal carbonyls), cyanide, or carbide, are generally considered to be organometallic as well.

Organic compound

In chemistry, many authors consider an organic compound to be any chemical compound that contains carbon-hydrogen or carbon-carbon bonds, however, some authors consider an organic compound to be any chemical compound that contains carbon. The definition of "organic" versus "inorganic" varies from author to author, and is a topic of debate. For example, methane () is considered organic, but whether some other carbon-containing compounds are organic or inorganic varies from author to author, for example halides of carbon without carbon-hydrogen and carbon-carbon bonds (e.