Building block libraries and structural considerations in the self-assembly of polyoxometalate and polyoxothiometalate systems

Inorganic metal-oxide clusters form a class of compounds that are unique in their topological and electronic versatility and are becoming increasingly more important in a variety of applications. Namely, Polyoxometalates (POMs) have shown an unmatched range of physical properties and the ability to form structures that can bridge several length scales. The formation of these molecular clusters is often ambiguous and is governed by self-assembly processes that limit our ability to rationally design such molecules. However, recent years have shown that by considering new building block principles the design and discovery of novel complex clusters is aiding our understanding of this process. Now with current progress in thiometalate chemistry, specifically polyoxothiometalates (POTM), the field of inorganic molecular clusters has further diversified allowing for the targeted development of molecules with specific functionality. This chapter discusses the main differences between POM and POTM systems and how this affects synthetic methodologies and reactivities. We will illustrate how careful structural considerations can lead to the generation of novel building blocks and further deepen our understanding of complex systems

Computer Aided Aroma Design. I. Molecular knowledge framework

Computer Aided Aroma Design (CAAD) is likely to become a hot issue as the REACH EC document targets many aroma compounds to require substitution. The two crucial steps in CAMD are the generation of candidate molecules and the estimation of properties, which can be difficult when complex molecular structures like odours are sought and when their odour quality are definitely subjective whereas their odour intensity are partly subjective as stated in Rossitier’s review (1996). In part I, provided that classification rules like those presented in part II exist to assess the odour quality, the CAAD methodology presented proceeds with a multilevel approach matched by a versatile and novel molecular framework. It can distinguish the infinitesimal chemical structure differences, like in isomers, that are responsible for different odour quality and intensity. Besides, its chemical graph concepts are well suited for genetic algorithm sampling techniques used for an efficient screening of large molecules such as aroma. Finally, an input/output XML format based on the aggregation of CML and ThermoML enables to store the molecular classes but also any subjective or objective property values computed during the CAAD process

Coarse-Graining Auto-Encoders for Molecular Dynamics

Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomistic simulations are often computationally unfeasible. Coarse-graining methods allow simulating larger systems, by reducing the dimensionality of the simulation, and propagating longer timesteps, by averaging out fast motions. Coarse-graining involves two coupled learning problems; defining the mapping from an all-atom to a reduced representation, and the parametrization of a Hamiltonian over coarse-grained coordinates. Multiple statistical mechanics approaches have addressed the latter, but the former is generally a hand-tuned process based on chemical intuition. Here we present Autograin, an optimization framework based on auto-encoders to learn both tasks simultaneously. Autograin is trained to learn the optimal mapping between all-atom and reduced representation, using the reconstruction loss to facilitate the learning of coarse-grained variables. In addition, a force-matching method is applied to variationally determine the coarse-grained potential energy function. This procedure is tested on a number of model systems including single-molecule and bulk-phase periodic simulations.Comment: 8 pages, 6 figure

Dendral-64 - a system for computer construction, enumeration and notation of organic molecules as tree structures and cyclic graphs. part i- notational algorithm for tree structures

Computer construction, enumeration, and notation of organic molecules as tree structures and cyclic graph

Cyclic β-glucans at the bacteria–host cells interphase: One sugar ring to rule them all

Cyclic β‐1,2‐D‐glucans (CβG) are natural bionanopolymers present in the periplasmic space of many Proteobacteria. These molecules are sugar rings made of 17 to 25 D‐glucose units linked exclusively by β‐1,2‐glycosidic bonds. CβG are important for environmental sensing and osmoadaptation in bacteria, but most importantly, they play key roles in complex host–cell interactions such as symbiosis, pathogenesis, and immunomodulation. In the last years, the identification and characterisation of the enzymes involved in the synthesis of CβG allowed to know in detail the steps necessary for the formation of these sugar rings. Due to its peculiar structure, CβG can complex large hydrophobic molecules, a feature possibly related to its function in the interaction with the host. The capabilities of the CβG to function as molecular boxes and to solubilise hydrophobic compounds are attractive for application in the development of drugs, in food industry, nanotechnology, and chemistry. More importantly, its excellent immunomodulatory properties led to the proposal of CβG as a new class of adjuvants for vaccine development.Fil: Guidolin, Leticia Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Arce Gorvel, Vilma. Centre National de la Recherche Scientifique; FranciaFil: Ciocchini, Andres Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Comerci, Diego José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina. Comisión Nacional de Energía Atómica. Centro Atómico Ezeiza; ArgentinaFil: Gorvel, Jean-Pierre. Centre National de la Recherche Scientifique; Franci

Flexibility in metal–organic frameworks : a basic understanding

Much has been written about the fundamental aspects of the metal-organic frameworks (MOFs). Still, details concerning the MOFs with structural flexibility are not comprehensively understood. However, a dramatic increase in research activities concerning rigid MOFs over the years has brought deeper levels of understanding for their properties and applications. Nonetheless, robustness and flexibility of such smart frameworks are intriguing for different research areas such as catalysis, adsorption, etc. This manuscript overviews the different aspects of framework flexibility. The review has touched lightly on several ideas and proposals, which have been demonstrated within the selected examples to provide a logical basis to obtain a fundamental understanding of their synthesis and behavior to external stimuli

Bacteriophages and their structural organisation

Viruses are extremely small infectious particles that are not visible in a light microscope, and are able to pass through fine porcelain filters. They exist in a huge variety of forms and infect practically all living systems: animals, plants, insects and bacteria. All viruses have a genome, typically only one type of nucleic acid, but it could be one or several molecules of DNA or RNA, which is surrounded by a protective stable coat (capsid) and sometimes by additional layers which may be very complex and contain carbohydrates, lipids, and additional proteins. The viruses that have only a protein coat are named “naked”, or non- enveloped viruses. Many viruses have an envelope (enveloped viruses) that wraps around the protein capsid. This envelope is formed from a lipid membrane of the host cell during the release of a virus out of the cell

Biporous Metal-Organic Framework with Tunable CO2/CH4 Separation Performance Facilitated by Intrinsic Flexibility.

In this work, we report the synthesis of SION-8, a novel metal-organic framework (MOF) based on Ca(II) and a tetracarboxylate ligand TBAPy4- endowed with two chemically distinct types of pores characterized by their hydrophobic and hydrophilic properties. By altering the activation conditions, we gained access to two bulk materials: the fully activated SION-8F and the partially activated SION-8P with exclusively the hydrophobic pores activated. SION-8P shows high affinity for both CO2 ( Qst = 28.4 kJ/mol) and CH4 ( Qst = 21.4 kJ/mol), while upon full activation, the difference in affinity for CO2 ( Qst = 23.4 kJ/mol) and CH4 ( Qst = 16.0 kJ/mol) is more pronounced. The intrinsic flexibility of both materials results in complex adsorption behavior and greater adsorption of gas molecules than if the materials were rigid. Their CO2/CH4 separation performance was tested in fixed-bed breakthrough experiments using binary gas mixtures of different compositions and rationalized in terms of molecular interactions. SION-8F showed a 40-160% increase (depending on the temperature and the gas mixture composition probed) of the CO2/CH4 dynamic breakthrough selectivity compared to SION-8P, demonstrating the possibility to rationally tune the separation performance of a single MOF by manipulating the stepwise activation made possible by the MOF's biporous nature