Are strong Brønsted acids necessarily strong Lewis acids?

Silicon Radical-Induced CH4 Dissociation for Uniform Graphene Coating on Silica Surface

Due to the manufacturability of highly well-defined structures and wide-range versatility in its microstructure, SiO2 is an attractive template for synthesizing graphene frameworks with the desired pore structure. However, its intrinsic inertness constrains the graphene formation via methane chemical vapor deposition. This work overcomes this challenge by successfully achieving uniform graphene coating on a trimethylsilyl-modified SiO2 (denote TMS-MPS). Remarkably, the onset temperature for graphene growth dropped to 720 °C for the TMS-MPS, as compared to the 885 °C of the pristine SiO2. This is found to be mainly from the Si radicals formed from the decomposition of the surface TMS groups. Both experimental and computational results suggest a strong catalytic effect of the Si radicals on the CH4 dissociation. The surface engineering of SiO2 templates facilitates the synthesis of high-quality graphene sheets. As a result, the graphene-coated SiO2 composite exhibits a high electrical conductivity of 0.25 S cm-1. Moreover, the removal of the TMP-MPS template has released a graphene framework that replicates the parental TMS-MPS template on both micro- and nano- scales. This study provides tremendous insights into graphene growth chemistries as well as establishes a promising methodology for synthesizing graphene-based materials with pre-designed microstructures and porosity.

OSCAR: an extensive repository of chemically and functionally diverse organocatalysts

The automated construction of datasets has become increasingly relevant in computational chemistry. While transition-metal catalysis has greatly benefitted from bottom-up or top-down strategies for the curation of organometallic complexes libraries, the field of organocatalysis is mostly dominated by case-by-case studies, with a lack of transferable data-driven tools that facilitate both the exploration of a wider range of catalyst space and the optimization of reaction properties. For these reasons, we introduce OSCAR, a repository of 4000 experimentally derived organocatalysts along with their corresponding building blocks and combinatorially enriched structures. We outline the fragment-based approach used for database generation and showcase the chemical diversity, in terms of functions and molecular properties, covered in OSCAR. The structures and corresponding stereoelectronic properties are publicly available (https://archive.materialscloud.org/record/2022.106) and constitute the starting point to build generative and predictive models for organocatalyst performance.

Elucidating the Reaction Mechanism of Atomic Layer Deposition of Al2O3 with a Series of Al(CH3)xCl3-x and Al(CyH2y+1)3 Precursors

The adsorption of metalorganic and metal halide precursors on the SiO₂ surface plays an essential role in thin-film deposition processes such as atomic layer deposition (ALD). In the case of aluminum oxide (Al₂O₃) films, the growth characteristics are influenced by the precursor structure, which controls both chemical reactivity and the geometrical constraints during deposition. In this work, a systematic study using a series of Al(CH₃)_xCl_3-x (x = 0, 1, 2, and 3) and Al(C_yH_2y+1)₃ (y = 1, 2, and 3) precursors is carried out using a combination of experimental spectroscopic techniques together with density functional theory calculations and Monte Carlo simulations to analyze differences across precursor molecules. Results show that reactivity and steric hindrance mutually influence the ALD surface reaction. The increase in the number of chlorine ligands in the precursor shifts the deposition temperature higher, an effect attributed to more favorable binding of the intermediate species due to higher Lewis acidity, while differences between precursors in film growth per cycle are shown to originate from variations in adsorption activation barriers and size-dependent saturation coverage. Comparison between the theoretical and experimental results indicates that the Al(C_yH_2y+1)₃ precursors are favored to undergo two ligand exchange reactions upon adsorption at the surface, whereas only a single Cl-ligand exchange reaction is energetically favorable upon adsorption by the AlCl₃ precursor. By pursuing the first-principles design of ALD precursors combined with experimental analysis of thin-film growth, this work enables a robust understanding of the effect of precursor chemistry on ALD processes.

Conceptual density functional theory based electronic structure principles

In this review article, we intend to highlight the basic electronic structure principles and various reactivity descriptors as defined within the premise of conceptual density functional theory (CDFT). Over the past several decades, CDFT has proven its worth in providing valuable insights into various static as well as time-dependent physicochemical problems. Herein, having briefly outlined the basics of CDFT, we describe various situations where CDFT based reactivity theory could be employed in order to gain insights into the underlying mechanism of several chemical processes.

Fast Determination of the Main Reduced Sulfur Species in Aquatic Systems by a Direct and Second-Derivative Spectrophotometric Method

The determination of reduced sulfur species in aquatic systems is not an easy and fast task to accomplish regarding the numerous possible interferences and risks of oxidation that occur with the usual methods of quantification. The method presented here is a direct spectrophotometric method that can be used to quantify sulfides, sulfites, and thiosulfates in a simple and rapid way. The principle is based on the comparison of second-derivative absorbance spectra of the same sample at different pH (9.2, 4.7, and 1.0) and selected absorption wavelengths (250 and 278 nm). This method has been successfully tested and has demonstrated liability to (i) avoid the biases due to absorbance overlaps between the different major chemical species and (ii) keep, as a direct method, the advantages over indirect methods on interferences reduction. The limits of detections (LOD) reached for total sulfide, sulfite, and thiosulfate are 1.37, 7.32, and 1.92 µM, respectively. The method displays low accuracy mean and low relative standard deviation (<4%) as well as a good linearity (R2 > 0.999). Accordingly, this method represents a very robust alternative in terms of cost and rapidity for the quantification of reduced sulfur species in different aquatic environments, from freshwaters to saline and polluted systems.

Chemical reactivity of the frustrated Lewis pairs in borophosphines: a theoretical analysis of their Lewis acidity, Lewis basicity and Fukui function

The chemical reactivity of a set of borophosphines of the general formula R₂B-G-PY₂, where G is the connector group between the Lewis acidic site, a borane group, and the Lewis basic site, a phosphine fragment, is theoretically investigated through their Lewis acidity and Lewis basicity, as well as the location of the Fukui function and the shape of the molecular electrostatic potential. The role of some global reactivity descriptors, like the vertical ionization potential, I, and the vertical electron affinity, A, is also analyzed in order to gain a deeper insight on the intrinsic chemical reactivity of these borophosphines. We also use the energies involved in the formation of the adducts between the borophosphine and the ions H^- and H⁺ to estimate the Lewis acidity and Lewis basicity, respectively; by their nature, these energies represent local reactivity descriptors. Some of these borophosphines are able to activate the covalent bond in the hydrogen molecule. Possible paths for the hydrogen release reaction from the zwitterion R[Formula: see text]HB-G-PH[Formula: see text] are studied using the mentioned quantities, suggesting that an intramolecular hydride shift mechanism seems to be more favorable than a proton migration process. The acceptor Fukui function f⁺(r) proved to be useful to identify the acidic molecular sites for the interaction with the hydride ion and the relative stability of the corresponding adducts is related to the relative values of this function.

4-Thiazolidinone coumarin derivatives as two-component NS2B/NS3 DENV flavivirus serine protease inhibitors: synthesis, molecular docking, biological evaluation and structure-activity relationship studies

A series of novel 4-thiazolidinone inhibitors SKYa-SKYg, containing coumarin as a core structure were synthesized via facile and efficient method. The structures of the synthesized compounds were established by extensive spectroscopic studies (FT IR, 1D NMR, 2D NMR, LC-MS) and elemental analysis. All the synthesized hybrids were further evaluated for their potential as anti-tubercular agents against Mycobacterium tuberculosis H37Rv ATCC 25618, and anti-bacterial agents against Escherichia coli, Enterobacter aerogenes, Salmonella typhi, Streptococcus pneumoniae and Staphylococcus aureus. Interestingly, the hybrids displayed potent bioactivity. However, compounds SKYc, SKYd, and SKYe appeared to be more effective against the tested bacterial strains, among which compound SKYb showed the highest inhibition against all the bacterial strains ranging from 41 to 165 μg/mL, as compared to the standards, streptomycin, kanamycin and vancomycin. Moreover, derivative SKYa was found to be the strongest against M. tuberculosis (83 μg/mL). Additionally, the anti-dengue potential of the coumarin hybrids as two-component NS2B/NS3 DENV flavivirus serine protease inhibitors was calculated using computational molecular docking approach, with reference to the standards 4-hydroxypanduratin, panduratin and ethyl 3-(4-(hydroxymethyl)-2-methoxy-5-nitrophenoxy)propanoate with DS of - 3.379, - 3.189 and - 3.381, respectively. The docking results revealed that the synthesized hybrids exhibited potent anti-dengue activity among which compounds SKYf, SKYd, SKYc and SKYe were found to be the best ones with docking scores of - 4.014, - 3.964, - 3.905 and - 3.889. In summary, we discovered 4-thiazolidinone coumarin derivatives as a new scaffold that may eventually yield useful compounds in the treatment of bacterial and viral infections.

Prediction of the Fate of Organic Compounds in the Environment From Their Molecular Properties: A Review

A comprehensive review of quantitative structure-activity relationships (QSAR) allowing the prediction of the fate of organic compounds in the environment from their molecular properties was done. The considered processes were water dissolution, dissociation, volatilization, retention on soils and sediments (mainly adsorption and desorption), degradation (biotic and abiotic), and absorption by plants. A total of 790 equations involving 686 structural molecular descriptors are reported to estimate 90 environmental parameters related to these processes. A significant number of equations was found for dissociation process (pKa), water dissolution or hydrophobic behavior (especially through the KOW parameter), adsorption to soils and biodegradation. A lack of QSAR was observed to estimate desorption or potential of transfer to water. Among the 686 molecular descriptors, five were found to be dominant in the 790 collected equations and the most generic ones: four quantum-chemical descriptors, the energy of the highest occupied molecular orbital (EHOMO) and the energy of the lowest unoccupied molecular orbital (ELUMO), polarizability (α) and dipole moment (μ), and one constitutional descriptor, the molecular weight. Keeping in mind that the combination of descriptors belonging to different categories (constitutional, topological, quantum-chemical) led to improve QSAR performances, these descriptors should be considered for the development of new QSAR, for further predictions of environmental parameters. This review also allows finding of the relevant QSAR equations to predict the fate of a wide diversity of compounds in the environment.

MOLECULAR ACIDITY OF BUILDING BLOCKS OF BIOLOGICAL SYSTEMS: A DENSITY FUNCTIONAL REACTIVITY THEORY STUDY

An accurate prediction of the molecular acidity by employing ab initio or density functional approaches for typical molecular systems is still challenging. Recently, we proposed to utilize two quantum descriptors, molecular electrostatic potential (MEP) and the sum of valence natural atomic orbital (NAO) energies on the nucleus of both the acidic atom and leaving proton, to quantitatively evaluate the pKa values. This new approach has been validated by a number of organic and inorganic systems and justified within the framework of density functional reactivity theory (DFRT). In this work, we apply the approach to building blocks of biological systems, namely, 20 natural α-amino acids and 5 DNA/RNA bases, together with a few other biologically relevant species. Our results show that there exists a strong linear correlation between MEP on the nucleus of the N atom and the sum of N 2p NAO energies, with the correlation coefficient R2 = 0.99. Also, we observe that both MEP on the nitrogen nucleus and the sum of N 2p NAO energies correlate well with experimental pKa values, with the correlation coefficient equal to 0.91. Using this established model, we predicted the trend of pKa changes of amino acids in proteins with different dielectric constants. We also applied the model to predict pKa values for dipeptides. Implications of these linear relationships to understand functions and reactivity of biological systems are discussed as well.

Protophilicity index and protofelicity equalization principle: new measures of Brønsted-Lowry-Lewis acid-base interactions

The simultaneous contributions of proton and electron transfer to the Brønsted-Lowry and Lewis acid-base properties of a set of p-substituted phenols are reported in this work. As a result of the analysis, a novel protophilicity index considered as the second-order energy change of a Brønsted-Lowry base as it is saturated with protons, a combined Brønsted-Lowry-Lewis acidity index (with a corresponding basicity index), and a protofelicity equalization principle (a parallel of the electronegativity equalization principle) are presented.

Molecular acidity: A quantitative conceptual density functional theory description

Accurate predictions of molecular acidity using ab initio and density functional approaches are still a daunting task. Using electronic and reactivity properties, one can quantitatively estimate pKa values of acids. In a recent paper [S. B. Liu and L. G. Pedersen, J. Phys. Chem. A 113, 3648 (2009)], we employed the molecular electrostatic potential (MEP) on the nucleus and the sum of valence natural atomic orbital (NAO) energies for the purpose. In this work, we reformulate these relationships on the basis of conceptual density functional theory and compare the results with those from the thermodynamic cycle method. We show that MEP and NAO properties of the dissociating proton of an acid should satisfy the same relationships with experimental pKa data. We employ 27 main groups and first to third row transition metal-water complexes as illustrative examples to numerically verify the validity of these strong linear correlations. Results also show that the accuracy of our approach and that of the conventional method through the thermodynamic cycle are statistically similar.

Estimation of molecular acidity via electrostatic potential at the nucleus and valence natural atomic orbitals

An effective approach of estimating molecular pK(a) values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pK(a) values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pK(a) data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pK(a) values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules.