pyCOFBuilder: A Python Package for Automated Creation of Covalent Organic Framework Models Based on the Reticular Approach.

Covalent organic frameworks (COFs) have gained significant popularity in recent years due to their unique ability to provide a high surface area and customizable pore geometry and chemistry, making them an ideal choice for a wide range of applications. However, exploring COFs experimentally can be arduous and time-consuming due to their immense number of potential structures. As a result, computational high-throughput studies have become an attractive option. Nevertheless, generating COF structures can also be a challenging and time-consuming task. To address this challenge, here, we introduce the pyCOFBuilder, an open-source Python package designed to facilitate the generation of COF structures for computational studies. The pyCOFBuilder software provides an easy-to-use set of functionalities to generate COF structures following the reticular approach. In this paper, we describe the implementation, main features, and capabilities of the pyCOFBuilder, demonstrating its utility for generating COF structures with varying topologies and chemical properties. pyCOFBuilder is freely available on GitHub at https://github.com/lipelopesoliveira/pyCOFBuilder.

Diastereoselectivity Switch During Alkene Reductions: Diastereodivergent Syntheses of Molecular Fossils via MHAT or Homogeneous Catalytic Hydrogenation Reactions.

Sixteen geosterane derivatives were synthesized in up to 57 % overall yields in four steps harnessing the olefin cross-metathesis (OCM) and Metal hydride H atom transfer (MHAT) or homogeneous hydrogenation reactions as key steps. Drawing on this strategy, the diastereomeric ratio (d. r.) reached up to 24 : 1 for the thermodynamic isomer and 7 : 1 for the other isomer in the hydrogenation step. In a geological sample from northeast Brazil, we confirmed the putative structures previously assumed as methyl 2-(3α-5αH-cholestan) acetate, methyl 2-(3ß-5αH-cholestan)acetate, and methyl 6-(3ß-5αH-cholestan)hexanoate, as well three new molecular fossils of approximately 120 million years old. We also proved the migration marking ability of those carboxylic acids derived from forerunner geosteranes during an oil migration event, which suggests their aptitudes as molecular odometers. Our approach demonstrated swiftness and effectiveness in preparing a molecular library of geological biomarkers would also be appropriate to generate stereochemical diversity in molecular libraries for medicinal chemistry and natural product anticipation.

Taming the Antiferromagnetic Beast: Computational Design of Ultrashort Mn-Mn Bonds Stabilized by N-Heterocyclic Carbenes.

The development of complexes featuring low-valent, multiply bonded metal centers is an exciting field with several potential applications. In this work, we describe the design principles and extensive computational investigation of new organometallic platforms featuring the elusive manganese-manganese bond stabilized by experimentally realized N-heterocyclic carbenes (NHCs). By using DFT computations benchmarked against multireference calculations, as well as MO- and VB-based bonding analyses, we could disentangle the various electronic and structural effects contributing to the thermodynamic and kinetic stability, as well as the experimental feasibility, of the systems. In particular, we explored the nature of the metal-carbene interaction and the role of the ancillary η6 coordination to the generation of Mn2 systems featuring ultrashort metal-metal bonds, closed-shell singlet multiplicities, and positive adiabatic singlet-triplet gaps. Our analysis identifies two distinct classes of viable synthetic targets, whose electrostructural properties are thoroughly investigated.

A Carbocationic Triarylmethane-Based Porous Covalent Organic Network.

A thermally stable carbocationic covalent organic network (CON), named RIO-70 was prepared from pararosaniline hydrochloride, an inexpensive dye, and triformylphloroglucinol in solvothermal conditions. This nanoporous organic material has shown a specific surface area of 990 m2 g-1 and pore size of 10.3 Å. The material has CO2 uptake of 2.14 mmol g-1 (0.5 bar), 2.7 mmol g-1 (1 bar), and 6.8 mmol g-1 (20 bar), the latter corresponding to 3 CO2 molecules adsorbed per pore per sheet. It is shown to be a semiconductor, with electrical conductivity (σ) of 3.17×10-7  S cm-1 , which increases to 5.26×10-4  S cm-1 upon exposure to I2 vapor. DFT calculations using periodic conditions support the findings.

Enzyme Immobilization in Covalent Organic Frameworks: Strategies and Applications in Biocatalysis.

The development of efficient catalytic systems is a fundamental aspect for the straightforward production of chemicals. During the last years, covalent organic frameworks (COFs) emerged as an exciting class of organic nanoporous materials. Due to their pre-designable structure, they can be prepared with distinct physicochemical characteristics, specific pore sizes, and tunable functional groups. Moreover, associated with their stability in different media, these materials are considered promising supports for enzyme immobilization. Herein, it is highlighted the recent literature of enzyme immobilization in COFs, the main immobilization strategies, and the catalytic applications of these composites.

Spiro-Carbon: A Metallic Carbon Allotrope Predicted from First Principles Calculations.

A structurally stable microporous metallic carbon allotrope, poly(spiro[2.2]penta-1,4-diyne) or, for short, spiro-carbon, with I41 /amd (D4h ) symmetry is predicted by first-principles calculations using density functional theory (DFT). The calculations of electronic, vibrational, and structural properties show that spiro-carbon has lower relative energy than other elusive carbon allotropes such as T-Carbon and 1-diamondyne (Y-Carbon). Its structure can be pictured as a set of trans-cisoid-polyacetylene chains tangled and interconnected together by sp3 carbon atoms. Calculations reveal a metallic electronic structure arising from an "intrinsic doping" of trans-cisoid-polyacetylene chains with sp3 carbon atoms. Possible synthetic routes and various simulated spectra (XRD, NMR, and IR absorption) are provided in order to guide future efforts to synthesize this novel material.

Design, Synthesis and Characterization of Nickel-Functionalized Covalent Organic Framework NiCl@RIO-12 for Heterogeneous Suzuki-Miyaura Catalysis.

A series of nickel-decorated covalent organic frameworks, NiCl@RIO-12, were prepared using the post-synthetic modification strategy, that is, by reacting NiCl2 with pristine RIO-12 under alkaline conditions. Interestingly, they retained their crystallinity and the amount of nickel incorporated could be tuned from 3.6 to 25 wt % according to the reaction conditions. The incorporation of a higher amount of nickel in NiCl@RIO-12 consistently led to a lower Brunauer-Emmett-Teller surface area. Additionally, no agglomeration of nickel particles was found and a relatively homogeneous dispersion of nickel could be ascertained by SEM and TEM-EDS. The paramagnetic material exhibited promising catalytic activity in Suzuki-Miyaura cross-coupling under microwave heating. Thus, NiCl@RIO-12 notably demonstrated good thermal stability and its recyclability showed no substantial loss of activity after 3 cycles.

Enzyme-Decorated Covalent Organic Frameworks as Nanoporous Platforms for Heterogeneous Biocatalysis.

Sustainability in chemistry heavily relies on heterogeneous catalysis. Enzymes, the main catalyst for biochemical reactions in nature, are an elegant choice to catalyze reactions due to their high activity and selectivity, although they usually suffer from lack of robustness. To overcome this drawback, enzyme-decorated nanoporous heterogeneous catalysts were developed. Three different approaches for Candida antarctica lipase B (CAL-B) immobilization on a covalent organic framework (PPF-2) were employed: physical adsorption on the surface, covalent attachment of the enzyme in functional groups on the surface and covalent attachment into a linker added post-synthesis. The influence of the immobilization strategy on the enzyme uptake, specific activity, thermal stability, and the possibility of its use through multiple cycles was explored. High specific activities were observed for PPF-2-supported CAL-B in the esterification of oleic acid with ethanol, ranging from 58 to 283 U mg-1 , which was 2.6 to 12.7 times greater than the observed for the commercial Novozyme 435.

Electronic structures of bisnoradamantenyl and bisnoradamantanyl dications and related species.

The highly pyramidalized molecule bisnoradamantene is extremely reactive toward nucleophiles and dienes. In this work, we studied the electronic structure of bisnoaradamantene, as well as those of its cation and dication, which are previously unreported carbonium ions. According to QTAIM and MO analysis, there is a 3c-2e bonding system in the bisnoradamantenyl cation and a 4c-2e bonding system in the bisnoradamantenyl dication. A topological study indicated that, on going from bisnoradamantene to its dication, π-bond interaction with the bridgehead carbon atom increases. Additional study of the bisnoradamantanyl dication also indicated that it has two multicenter bonding systems. Comparison of the D3BIA and NICS aromaticity indices of these molecules and other derivatives indicates that these indices are well correlated, and analysis of these indices shows that the cationic and dicationic bisnoradamantenyl species are homoaromatic.

Alkane activation over acidic zeolites: the first step.

The heterogeneous acid-catalyzed activation step of alkanes leading to the reaction intermediates (carbocationic or alkoxy species) was up to now the matter of a longstanding controversy. Gas chromatography and online mass spectroscopy measurements show that H(2) and methane are formed over H-zeolites, whereas HD and CH(3)D are formed over D-zeolites as the primary products in the reaction with isobutane. These results indicate that sigma-bond protolysis by strong acid sites is the first step for hydrocarbon activation on these catalysts at mild temperatures (473 K), in analogy to the activation path occurring in liquid superacid media.

The three-component biginelli reaction: a combined experimental and theoretical mechanistic investigation.

Biginelli reactions have been monitored by direct infusion electrospray ionization mass spectrometry (ESI-MS) and key cationic intermediates involved in this three-component reaction have been intercepted and further characterized by tandem MS experiments (ESI-MS/MS). Density functional theory calculations were also used to investigate the feasibility of the major competing mechanisms proposed for the Biginelli reaction. The experimental and theoretical results were found to corroborate the iminium mechanism proposed by Folkers and Johnson, whereas no intermediates directly associated with either the more energy demanding Knoevenagel or enamine mechanisms could be intercepted.

Derivatives of spiropentadiene dication: new species with planar tetracoordinate carbon (ptC) atom.

In this work, nine tetrasubstituted derivatives [NH(2), OCH(3), Li, Na, Si(CH(3))(3)/SiH(2)CH(3,) P(CH(3))(2), Cl, F, and CN] of the spiropentadiene dication were analyzed within the framework of QTAIM. In the studied series, the electron-withdrawing substituents destabilize the ptC-containing spiropentadiene dication. On the other hand, stabilization of this dication is possible for electron-donating substituents only through sigma bonds, such as Li and Na. In all studied systems, according to QTAIM, the pi-electron system does not participate in the stabilization of the ptC atom in the spiropentadiene dication. sigma-electron-donating groups stabilize the spiropentadiene dication system by increasing the charge density of C(ext)-ptC bonds, whereas electron-withdrawing groups remove the charge density from C(ext)-ptC bonds.

Superacid-promoted reactions of alpha-ketoamides and related systems.

The superacid-promoted reactions of alpha-hydroxy and alpha-ketoamides have been studied. Ionization of these compounds leads to varied aryl-substituted oxyindole products. In some cases, electrocyclization can lead to substituted fluorene products. Dicationic, superelectrophilic intermediates are proposed as intermediates leading to the products from alpha-hydroxy and alpha-ketoamides.

Anisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluation.

Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental (1)H and (13)C NMR (in CDCl(3), CD(3)OD, and DMSO-d(6) solvents) and in some cases with good correlation to theoretical (1)H and (13)C NMR DFT-GIAO (B3LYP/6-311++G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an N-CH(2) moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied.

Electronic nature of carbonium ions and their silicon analogues.

Nonclassical ions or carbonium ions have multi-center bonding from delocalized sigma or pi electrons. The 2-norbornyl cation, its derivative 6,6-difluoro-2-norbornyl cation, tris-homocyclopropenyl cation, 7-norbornenyl cation, and 4-cyclopentenyl cation and their corresponding silicon analogues were studied in this work. All carbocations have topologically different 3c-2e systems. The magnitude of all delocalization indexes between each atomic pair of the 3c-2e bond can be used to predict homoaromaticity. The silicon analogues have a topologically different 3c-2e bond from their corresponding carbocation.

Understanding the planar tetracoordinate carbon atom: spiropentadiene dication.

The atoms in molecule theory shows that the spiropentadiene dication has a planar tetracoordinate carbon (ptC) atom stabilized mainly through the sigma bonds and this atom has a negative charge. The bonds to the ptC atom have less covalent character than the central carbon from neutral spiropentadiene. The total positive charge is spread along the structure skeleton. The analysis of the potential energy surface shows that the dication spiropentadiene has a 2.3 kcal/mol activation barrier for ring opening.

Electronic nature of planar cyclobutenyl dication derivatives.

The cyclobutadiene dication was not experimentally characterized to the date. However, some of its derivatives were. Most of them have planar geometry, but tetramethylcyclobutadiene dication has a nonplanar geometry according to ab initio calculations. From the atoms in molecules (AIM) theoretical analysis, common electronic features for the planar and puckered cyclobutenyl dication derivatives were observed. The planar cyclobutenyl dication derivatives have bond order of chemical bonds in the ring close to unity and relatively small electronic density in the ring. The puckered cyclobutadiene dication and its puckered derivatives have relatively high electronic density in the ring.

Aza-Nazarov reaction and the role of superelectrophiles.

The superacid-catalyzed reactions of N-acyliminium ion salts have been studied. The new conversions are remarkably similar to the Nazarov reaction and dicationic superelectrophilic species are thought to be involved. Experimental studies show that the cyclizations may be used to prepare varied heterocyclic products, while theoretical studies show that formation of the superelectrophiles can lead to very favorable reaction energetics.

Nature of the chemical bond in protonated methane.

Protonated methane, CH(5)(+), is a key reactive intermediate in hydrocarbon chemistry and a borderline case for chemical structure theory, being the simplest example of hypercoordinated carbon. Early quantum mechanical calculations predicted that the properties of this species could not be associated with only one structure, because it presents serious limitations of the Born-Oppenheimer approximation. However, ab initio molecular dynamics and diffusion Monte Carlo calculations showed that the most populated structure could be pictured as a CH(3) tripod linked to a H(2) moiety. Despite this controversy, a model for the chemical bonds involved in this ion still lacks. Here we present a modern valence bond model for the electronic structure of CH(5)(+). The chemical bond scheme derived directly from our calculations pictures this ion as H(3)C...H(2)(+). The fluxionality can be seen as the result of a proton transfer between C-H bonds. A new insight on the vibrational bands at approximately 2400 and approximately 2700 cm(-1) is suggested. Our results show that the chemical bond model can be profitably applied to such intriguing systems.