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.

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.

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.

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.

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.

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.

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.

Experimental and DFT study of the partial oxidation of benzene by N2O over H-ZSM-5: acid catalyzed mechanism.

The reaction mechanism for hydroxylation of benzene by N(2)O has been studied on chemically modified ZSM-5 catalysts. A maximum in catalytic activity and selectivity was reached for steamed samples under mild conditions (about 30% conversion with 94% selectivity). Chemical modifications, through ion exchange (H(+) versus Na(+)), have demonstrated the importance of the presence of Brönsted acid sites. The results obtained suggest a Langmuir-Hinshelwood mechanism between benzene and N(2)O adsorbed on two distinct active sites. A density functional theory study considering the possible reaction intermediates also confirmed the possible formation of protonated nitrous oxide, leading to a Wheland-type intermediate, thus supporting an electrophilic aromatic substitution assisted by the confined environment provided by the active zeolite framework.

Electrophilic aromatic nitration: understanding its mechanism and substituent effects.

Theoretical calculations and gas-phase mass spectrometric studies were performed for the reaction of the naked (NO2+) and monosolvated (CH3NO2.NO2+) nitronium ion with several monosubstituted aromatic compounds. From these studies, we propose a general model for regioselectivity based on the single-electron transfer (SET) mechanism and an alternative mechanistic scheme for electrophilic aromatic nitration. This scheme considers the SET and the polar (Ingold-Hughes) mechanisms as extremes in a continuum pathway, the occurrence and extents of both mechanisms being governed mainly by the ability, or lack of ability, of the aromatic compound to transfer an electron to NO2+.

Allenediazonium ions and their protonation chemistry: a DFT study.

The parent allenediazonium monocation H2C[double bond]C[double bond]CH(N2+) and ten of its substituted derivatives XYC[double bond]C[double bond]C(Z)N2+ (with F, CF3, Me, OMe, and Me2N as substituents) were studied by DFT at the B3LYP/6-31++G** level. Except for the Me2N-substituted derivative that forms a monocation-N2 complex, structurally intact allenediazonium ions were obtained as minima in all cases. Protonation studies at various sites were performed on allenediazonium cations, and relative energies of the resulting minima were used to identify the energetically most favored dications. In the majority of cases, protonation at the central carbon of the allenic moiety (C2) is most favored, forming delocalized allyl cation-N2+ species. The same dication structure is formed via initial C3-protonation, followed by a formal hydride shift, in cases where a carbocation-stabilizing group is placed at C3. When a CF3 group is placed at C3, initial protonation at C1 resulted in a 1,3-fluorine shift, to generate a fluoroallyl cation linked to a CH2N2+ moiety. Structural features in the allenediazonium monocations and their protonated dications were examined, taking into account their geometrical features, computed charges, and the GIAO NMR shifts.

Neutral structures with a planar tetracoordinated carbon based on spiropentadiene analogues.

Neutral hydrocarbon structures containing a planar tetracoordinated carbon atom are proposed on the basis of quantum chemical calculations. The planarity at the central carbon atom is achieved by using aromaticity for stabilizing a positively charged core moiety that contains the planar atom. This charge is compensated by negatively charged cyclopentadienyl rings fused on the structure, leading to neutral structures. These are found to be stable from a dynamic point of view and are potentially synthesizable through carbene chemistry. These structures can lead to new breakthroughs in the chemical structure theory. A family of species derived from this model is also presented.

The nature of superacid electrophilic species in HF/SbF(5): a density functional theory study.

A density functional theory study at the B3LYP/6-31++G** + RECP(Sb) level of the HF/SbF(5) superacid system was carried out. The geometries of possible electrophilic species, such as H(2)F(+).Sb(2)F(11)(-) and H(3)F(2)(+).Sb(2)F(11)(-), were calculated and correspond with available experimental results. Calculations of different equilibrium reactions involving HF and SbF(5) allowed the relative concentration of the most energetically favorable species present in 1:1 HF/SbF(5) solutions to be estimated. These species are H(+).Sb(2)F(11)(-), H(2)F(+).Sb(2)F(11)(-), H(3)F(2)(+).Sb(2)F(11)(-), and H(4)F(3)(+).Sb(2)F(11)(-), which correspond to 36.9, 16.8, 36.9, and 9.4%, respectively. Calculations of the acid strength of the electrophilic species were also performed and indicated that, for the same anion, the acid strength increases with the solvation degree. The entropic term also plays a significant role in proton-transfer reactions in superacid systems.