Computational Discovery of Molecular C60 Encapsulants with an Evolutionary Algorithm

2019 ◽  
Author(s):  
Marcin Miklitz ◽  
Lukas Turcani ◽  
Rebecca L. Greenaway ◽  
Kim Jelfs
Keyword(s):  
Evolutionary Algorithm ◽  
Chemical Space ◽  
Fitness Function ◽  
Building Blocks ◽  
Fullerene C60 ◽  
Cavity Size ◽  
Structural Symmetry ◽  
Wide Range ◽  
Material Systems ◽  
Computational Discovery

<p>A function-led computational discovery using an evolutionary algorithm was used to find potential fullerene (C60) encapsulants within the chemical space of porous organic cages. This makes use of a tailored fitness function that includes consideration of the interaction energy between the cage and the C60 molecule, the shape persistence of the cage, and the symmetry of the assemblies. We find that the promising host cages for C60 evolve over the simulations towards systems that share features such as the correct cavity size to host C60, planar tri-topic aldehyde building blocks with a small number of rotational bonds, di-topic amine linkers with functionality on adjacent carbon atoms, high structural symmetry, and strong complex binding affinity towards C60. The proposed cages are chemically feasible and similar to cages already present in the literature, helping to increase the likelihood of the future synthetic realisation of these predictions. The presented approach is highly generalisable and can be tailored to target a wide range of properties in molecular encapsulants or other molecular material systems.</p>

Computational Discovery of Molecular C60 Encapsulants with an Evolutionary Algorithm

2019 ◽  
Author(s):  
Marcin Miklitz ◽  
Lukas Turcani ◽  
Rebecca L. Greenaway ◽  
Kim Jelfs
Keyword(s):  
Evolutionary Algorithm ◽  
Chemical Space ◽  
Fitness Function ◽  
Building Blocks ◽  
Fullerene C60 ◽  
Cavity Size ◽  
Structural Symmetry ◽  
Wide Range ◽  
Material Systems ◽  
Computational Discovery

<p>A function-led computational discovery using an evolutionary algorithm was used to find potential fullerene (C60) encapsulants within the chemical space of porous organic cages. This makes use of a tailored fitness function that includes consideration of the interaction energy between the cage and the C60 molecule, the shape persistence of the cage, and the symmetry of the assemblies. We find that the promising host cages for C60 evolve over the simulations towards systems that share features such as the correct cavity size to host C60, planar tri-topic aldehyde building blocks with a small number of rotational bonds, di-topic amine linkers with functionality on adjacent carbon atoms, high structural symmetry, and strong complex binding affinity towards C60. The proposed cages are chemically feasible and similar to cages already present in the literature, helping to increase the likelihood of the future synthetic realisation of these predictions. The presented approach is highly generalisable and can be tailored to target a wide range of properties in molecular encapsulants or other molecular material systems.</p>

Computational Discovery of Molecular C60 Encapsulants with an Evolutionary Algorithm

2019 ◽  
Author(s):  
Marcin Miklitz ◽  
Lukas Turcani ◽  
Rebecca L. Greenaway ◽  
Kim Jelfs
Keyword(s):  
Evolutionary Algorithm ◽  
Chemical Space ◽  
Fitness Function ◽  
Building Blocks ◽  
Fullerene C60 ◽  
Cavity Size ◽  
Structural Symmetry ◽  
Wide Range ◽  
Material Systems ◽  
Computational Discovery

<p>A function-led computational discovery using an evolutionary algorithm was used to find potential fullerene (C60) encapsulants within the chemical space of porous organic cages. This makes use of a tailored fitness function that includes consideration of the interaction energy between the cage and the C60 molecule, the shape persistence of the cage, and the symmetry of the assemblies. We find that the promising host cages for C60 evolve over the simulations towards systems that share features such as the correct cavity size to host C60, planar tri-topic aldehyde building blocks with a small number of rotational bonds, di-topic amine linkers with functionality on adjacent carbon atoms, high structural symmetry, and strong complex binding affinity towards C60. The proposed cages are chemically feasible and similar to cages already present in the literature, helping to increase the likelihood of the future synthetic realisation of these predictions. The presented approach is highly generalisable and can be tailored to target a wide range of properties in molecular encapsulants or other molecular material systems.</p>

scholarly journals An Evolutionary Algorithm for the Discovery of Porous Organic Cages

2018 ◽  
Author(s):  
Enrico Berardo ◽  
Lukas Turcani ◽  
Marcin Miklitz ◽  
Kim Jelfs
Keyword(s):  
Phase Space ◽  
Evolutionary Algorithm ◽  
Pore Size ◽  
Building Block ◽  
Chemical Space ◽  
Building Blocks ◽  
Cavity Size ◽  
Supramolecular Materials ◽  
Molecular Separation ◽  
Efficient Exploration

The phase space of possible supramolecular materials is enormous, as they can, in principle, be built from any combination of organic building blocks. Here we have developed an evolutionary algorithm (EA) that can assist in the efficient exploration of chemical space for supramolecules, helping to guide synthesis to materials with promising applications. We demonstrate the utility of our EA to porous organic cages, predicting both promising targets and identifying the chemical features that emerge as important for a cage to be shape persistent or to adopt a particular cavity size. We identify that shape persistent cages require a low percentage of rotatable bonds in their precursors (<20%) and that the higher topicity building block in particular should use <p>double bonds for rigidity. We can use the EA to explore what size ranges for precursors are required for achieving a given pore size in a cage and show that 16 Å pores, which are absent in the literature, should be synthetically achievable. Our EA implementation is adaptable and easily extendable, not only to target specific properties of porous</p> <p>organic cages, such as optimal encapsulants or molecular separation materials, but also to any easily calculable property of other supramolecular materials.</p>

scholarly journals An Evolutionary Algorithm for the Discovery of Porous Organic Cages

2018 ◽  
Author(s):  
Enrico Berardo ◽  
Lukas Turcani ◽  
Marcin Miklitz ◽  
Kim Jelfs
Keyword(s):  
Phase Space ◽  
Evolutionary Algorithm ◽  
Pore Size ◽  
Building Block ◽  
Chemical Space ◽  
Building Blocks ◽  
Cavity Size ◽  
Supramolecular Materials ◽  
Molecular Separation ◽  
Efficient Exploration

The phase space of possible supramolecular materials is enormous, as they can, in principle, be built from any combination of organic building blocks. Here we have developed an evolutionary algorithm (EA) that can assist in the efficient exploration of chemical space for supramolecules, helping to guide synthesis to materials with promising applications. We demonstrate the utility of our EA to porous organic cages, predicting both promising targets and identifying the chemical features that emerge as important for a cage to be shape persistent or to adopt a particular cavity size. We identify that shape persistent cages require a low percentage of rotatable bonds in their precursors (<20%) and that the higher topicity building block in particular should use <p>double bonds for rigidity. We can use the EA to explore what size ranges for precursors are required for achieving a given pore size in a cage and show that 16 Å pores, which are absent in the literature, should be synthetically achievable. Our EA implementation is adaptable and easily extendable, not only to target specific properties of porous</p> <p>organic cages, such as optimal encapsulants or molecular separation materials, but also to any easily calculable property of other supramolecular materials.</p>

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

Stereospecific, Palladium-catalyzed C(sp3)–H Alkenylation and Alkynylation of a Proline Derivative Enabled by 8-Aminoquinoline as a Directing Group

2020 ◽  
Author(s):  
Aleksandra Balliu ◽  
Aaltje Roelofje Femmigje Strijker ◽  
Michael Oschmann ◽  
Monireh Pourghasemi Lati ◽  
Oscar Verho
Keyword(s):  
Carboxylic Acid ◽  
Building Blocks ◽  
Wide Range ◽  
Palladium Catalyzed ◽  
Directing Group ◽  
High Yields ◽  
Vinyl Iodides ◽  
Initial Results

<p>In this preprint, we present our initial results concerning a stereospecific Pd-catalyzed protocol for the C3 alkenylation and alkynylation of a proline derivative carrying the well utilized 8‑aminoquinoline directing group. Efficient C–H alkenylation was achieved with a wide range of vinyl iodides bearing different aliphatic, aromatic and heteroaromatic substituents, to furnish the corresponding C3 alkenylated products in good to high yields. In addition, we were able show that this protocol can also be used to install an alkynyl group into the pyrrolidine scaffold, when a TIPS-protected alkynyl bromide was used as the reaction partner. Furthermore, two different methods for the removal of the 8-aminoquinoline auxiliary are reported, which can enable access to both <i>cis</i>- and <i>trans</i>-configured carboxylic acid building blocks from the C–H alkenylation products.</p>

Efficient Prediction of Structural and Electronic Properties of Hybrid 2D Materials Using DFT and Machine Learning

2018 ◽  
Author(s):  
Sherif Tawfik ◽  
Olexandr Isayev ◽  
Catherine Stampfl ◽  
Joseph Shapter ◽  
David Winkler ◽  
...  
Keyword(s):  
Machine Learning ◽  
Band Gap ◽  
Density Functional ◽  
2D Materials ◽  
Van Der Waals ◽  
Building Blocks ◽  
Machine Learning Techniques ◽  
Interlayer Distance ◽  
Computational Screening ◽  
Wide Range

Materials constructed from different van der Waals two-dimensional (2D) heterostructures offer a wide range of benefits, but these systems have been little studied because of their experimental and computational complextiy, and because of the very large number of possible combinations of 2D building blocks. The simulation of the interface between two different 2D materials is computationally challenging due to the lattice mismatch problem, which sometimes necessitates the creation of very large simulation cells for performing density-functional theory (DFT) calculations. Here we use a combination of DFT, linear regression and machine learning techniques in order to rapidly determine the interlayer distance between two different 2D heterostructures that are stacked in a bilayer heterostructure, as well as the band gap of the bilayer. Our work provides an excellent proof of concept by quickly and accurately predicting a structural property (the interlayer distance) and an electronic property (the band gap) for a large number of hybrid 2D materials. This work paves the way for rapid computational screening of the vast parameter space of van der Waals heterostructures to identify new hybrid materials with useful and interesting properties.

General Cyclopropane Assembly via Enantioselective Redox-Active Carbene Transfer to Aliphatic Olefins

2018 ◽  
Author(s):  
Marc Montesinos-Magraner ◽  
Matteo Costantini ◽  
Rodrigo Ramirez-Contreras ◽  
Michael E. Muratore ◽  
Magnus J. Johansson ◽  
...  
Keyword(s):  
Total Synthesis ◽  
Asymmetric Synthesis ◽  
Chemical Space ◽  
Synthetic Approach ◽  
Asymmetric Cyclopropanation ◽  
Redox Active ◽  
Wide Range ◽  
Leaving Group ◽  
Stereoelectronic Properties ◽  
Carbene Transfer

Asymmetric cyclopropane synthesis currently requires bespoke strategies, methods, substrates and reagents, even when targeting similar compounds. This limits the speed and chemical space available for discovery campaigns. Here we introduce a practical and versatile diazocompound, and we demonstrate its performance in the first unified asymmetric synthesis of functionalized cyclopropanes. We found that the redox-active leaving group in this reagent enhances the reactivity and selectivity of geminal carbene transfer. This effect enabled the asymmetric cyclopropanation of a wide range of olefins including unactivated aliphatic alkenes, enabling the 3-step total synthesis of (–)-dictyopterene A. This unified synthetic approach delivers high enantioselectivities that are independent of the stereoelectronic properties of the functional groups transferred. Our results demonstrate that orthogonally-differentiated diazocompounds are viable and advantageous equivalents of single-carbon chirons<i>.</i>

Application of Nitrogen Heterocyclic Carbenes in Organocatalysis

2020 ◽  
Vol 09 ◽  
Author(s):  
Minita Ojha ◽  
R. K. Bansal
Keyword(s):  
Asymmetric Catalysis ◽  
Building Blocks ◽  
Structural Features ◽  
Heterocyclic Carbenes ◽  
Stetter Reaction ◽  
Metal Pollutants ◽  
Synthetic Strategy ◽  
Wide Range ◽  
Benzoin Condensation ◽  
Nitrogen Heterocyclic

Background: During the last two decades, horizon of research in the field of Nitrogen Heterocyclic Carbenes (NHC) has widened remarkably. NHCs have emerged as ubiquitous species having applications in a broad range of fields, including organocatalysis and organometallic chemistry. The NHC-induced non-asymmetric catalysis has turned out to be a really fruitful area of research in recent years. Methods: By manipulating structural features and selecting appropriate substituent groups, it has been possible to control the kinetic and thermodynamic stability of a wide range of NHCs, which can be tolerant to a variety of functional groups and can be used under mild conditions. NHCs are produced by different methods, such as deprotonation of Nalkylhetrocyclic salt, transmetallation, decarboxylation and electrochemical reduction. Results: The NHCs have been used successfully as catalysts for a wide range of reactions making a large number of building blocks and other useful compounds accessible. Some of these reactions are: benzoin condensation, Stetter reaction, Michael reaction, esterification, activation of esters, activation of isocyanides, polymerization, different cycloaddition reactions, isomerization, etc. The present review includes all these examples published during the last 10 years, i.e. from 2010 till date. Conclusion: The NHCs have emerged as versatile and powerful organocatalysts in synthetic organic chemistry. They provide the synthetic strategy which does not burden the environment with metal pollutants and thus fit in the Green Chemistry.

Regioselective Functionalization of N-Fused Heteroaromatics via FeCl3-Catalyzed Nucleophilic Addition to Activated N-Heterocycles

Synthesis ◽  
2020 ◽  
Author(s):  
Ikyon Kim ◽  
Sung June Kim ◽  
Sunhee Lee
Keyword(s):  
Aromatic Compounds ◽  
Nucleophilic Addition ◽  
Chemical Space ◽  
Wide Range ◽  
Regioselective Functionalization

AbstractBroadening of nitrogen-fused heteroaromatic chemical space such as indolizine and pyrrolo[1,2-a]pyrazine was achieved via FeCl­3-catalyzed nucleophilic addition of these N-fused aromatic compounds to a wide range of azolinium systems generated in situ, leading to novel N-fused heteroaromatic scaffolds with dearomatized N-heterocyclic substituents regioselectively. Nucleophilic addition of indolizines and pyrrolo[1,2-a]pyrazines mainly occurred at the C1 position of the isoquinoliniums and at the C4 site of the quinoliniums.

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