An automated molecular porosity detection approach was developed and applied to PubChem, a repository of ca. 94 million molecules, to discover intrinsically porous cage molecules, which, although ...previously considered by chemists, have remained in oblivion to the porous solids community as neither their crystal structures nor solid-state porosity have been previously reported. The effort led to identification of six such cage molecules reported over the span of the last two decades. The following crystal structure prediction effort suggested that these molecules can form stable low-energy porous crystalline phases. One of the identified lowest energy phases exhibits zeolite-range porosity with pore diameters of ca. 8 Å and internal surface area of 1070 m2/g.
The cover image is based on the Software Focus AQME: Automated quantum mechanical environments for researchers and educators by Juan V. Alegre‐Requena et al., https://doi.org/10.1002/wcms.1663.
Porous molecular materials based on imine cages are prototyped for applications such as gas separations, water purification and others. Among tens of imine cages that have been synthesized so far, ...ones supporting large pore materials for high-flux membrane applications are rare due to the natural tendency of atoms and molecules to favor high-density arrangements. Here, we present a computational approach leading to identification of a large rigid imine cage molecule, which is based on 1,3,5-triformylbenzene and adamantane-1,3-diamine precursors. Through density functional theory-based crystal structure prediction, we demonstrate that this cage supports a number of synthetically-accessible porous crystal phases characterized by pore limiting diameters in the range of 3.5-5.5 Å. Furthermore, we demonstrate that the new cage molecule also supports a highly porous amorphous phase enabling a high-flux reverse-osmosis membrane application. Our molecular simulation-based investigation of the latter membrane in a water desalination scenario suggests that the new material can offer more than 100% increase in water flux over the benchmark porous Covalent Cage 3 (CC3) material.
Design of both crystalline and amorphous porous molecular solids based on a large imine cage molecule.
La investigación buscó establecer la incidencia de la vigilancia ambiental en la prevención de riesgos ambientales en las empresas industriales pesqueras de Tacna. Es una investigación no ...experimental, transversal, que comprendió una muestra no probabilística intencional de personal de producción (n=42) de industrias del sector pesquero de la región. Se utilizaron dos cuestionarios, validados a través de juicio de expertos y se estimó la confiabilidad con el Alfa de Cronbach. Como resultados se conoció que los participantes perciben en su mayoría, que la vigilancia ambiental (planta de congelado, curado, enlatado) es baja (45,2%), predomina una percepción de vigilancia ambiental regular en la planta de consumo indirecto de harina de residuos. La prevención de riesgos ambientales se percibe en su mayoría regular (45,2%). Se concluye que la vigilancia ambiental incide en la prevención de los riesgos ambientales en las empresas pesqueras de Tacna.
DFT calculations and microkinetic simulations are applied to the reproduction of previously reported experimental results on the evolution of product concentration versus time in the condensation ...reaction of n-butylamine and benzaldehyde. The mechanism is complicated by the role played by water impurities as proton shuttles. Several functionals and other approaches are tested, yet good agreement is only achieved upon the usage of an adjustment consisting of a directed biasing of the computed DFT free energies.
Metal-catalyzed propargylic transformations represent a powerful tool in organic synthesis to achieve new carbon–carbon and carbon–heteroatom bonds. However, detailed knowledge about the mechanistic ...intricacies related to the asymmetric formation of propargylic products featuring challenging heteroatom-substituted tertiary stereocenters is scarce and therefore provides an inspiring challenge. Here, we present a meticulous mechanistic analysis of a propargylic sulfonylation reaction promoted by a chiral Cu catalyst through a combination of experimental techniques and computational studies. Surprisingly, the enantio-discriminating step is not the coupling between the nucleophile and the propargylic precursor but rather the following proto-demetalation step, a scenario further validated by computing enantio-induction levels under other previously reported experimental conditions. A full mechanistic scenario for this propargylic substitution reaction is provided, including a catalyst pre-activation stage, a productive catalytic cycle, and an unanticipated non-linear effect at the Cu(I) oxidation level.
Abstract
AQME, automated quantum mechanical environments, is a free and open‐source Python package for the rapid deployment of automated workflows using cheminformatics and quantum chemistry. AQME ...workflows integrate tasks performed across multiple computational chemistry packages and data formats, preserving all computational protocols, data, and metadata for machine and human users to access and reuse. AQME has a modular structure of independent modules that can be implemented in any sequence, allowing the users to use all or only the desired parts of the program. The code has been developed for researchers with basic familiarity with the Python programming language. The CSEARCH module interfaces to molecular mechanics and semi‐empirical QM (SQM) conformer generation tools (e.g., RDKit and Conformer–Rotamer Ensemble Sampling Tool, CREST) starting from various initial structure formats. The CMIN module enables geometry refinement with SQM and neural network potentials, such as ANI. The QPREP module interfaces with multiple QM programs, such as Gaussian, ORCA, and PySCF. The QCORR module processes QM results, storing structural, energetic, and property data while also enabling automated error handling (i.e., convergence errors, wrong number of imaginary frequencies, isomerization, etc.) and job resubmission. The QDESCP module provides easy access to QM ensemble‐averaged molecular descriptors and computed properties, such as NMR spectra. Overall, AQME provides automated, transparent, and reproducible workflows to produce, analyze and archive computational chemistry results. SMILES inputs can be used, and many aspects of tedious human manipulation can be avoided. Installation and execution on Windows, macOS, and Linux platforms have been tested, and the code has been developed to support access through Jupyter Notebooks, the command line, and job submission (e.g., Slurm) scripts. Examples of pre‐configured workflows are available in various formats, and hands‐on video tutorials illustrate their use.
This article is categorized under:
Data Science > Chemoinformatics
Data Science > Computer Algorithms and Programming
Software > Quantum Chemistry
The direct functionalization of Si–H bonds by the nitrene insertion methodology is described. A copper(I) complex bearing a trispyrazolylborate ligand catalyzes the transfer of a nitrene group from ...PhINTs to the Si–H bond of silanes, disilanes, and siloxanes, leading to the exclusive formation of Si–NH moieties in the first example of this transformation. The process tolerates other functionalities in the substrate such as several C–H bonds and alkyne and alkene moieties directly bonded to the silicon center. Density functional theory (DFT) calculations provide a mechanistic interpretation consisting of a Si–H homolytic cleavage and subsequent rebound to the Si-centered radical.
The ground electronic state potential energy surface of acryloyl chloride, CH
2
CHC(O)Cl, has been mapped using an automated transition state search procedure. A total of 174 minima, 527 TSs, and 20 ...different dissociation channels have been found. Among others, three novel HCl elimination pathways, namely, a five-center mechanism and two three-body dissociations (leading to CO + HCl + HCCH) have been discovered. While the bimodal character of the experimental HCl rotational distributions was previously attributed to the presence of two competing channels, our dynamics simulations show that a single channel, the four-center HCl elimination of CH
2
ClCHCO following a 1,3-Cl-shift of CH
2
CHC(O)Cl, displays a bimodal distribution in nearly prefect agreement with the experiment. Overall, our simulation results suggest that, as far as molecular elimination is concerned, this channel dominates in the 193 nm photodissociation of the molecule. The simulations also show evidence of non-IRC dynamics for this channel.
The use of an automated TS search method leads to the finding of novel HCl elimination pathways.
In the study of chemical processes, visualizing reaction networks is pivotal for identifying crucial compounds and transformations. Traditional methods, such as network schematics and reaction path ...linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity. Alternatives capable of leading with complexity include graph methods, but they are not user-friendly, lacking simplicity and modularity, which hinders their integration with widely-used research software. This work introduces rNets an innovative tool designed for the efficient visualization of reaction networks with a user-friendly interface, modularity, and seamless integration with existing software packages. The effectiveness of rNets is demonstrated through its application in analyzing three catalytic reactions, showcasing its potential to significantly enhance research both in homogeneous and heterogeneous catalysis fields. This tool not only simplifies the visualization process but also opens new avenues for exploring complex reaction networks in diverse research contexts.
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