Introducing SpectraFit: An Open-Source Tool for Interactive Spectral Analysis.

In chemistry, analyzing spectra through peak fitting is a crucial task that helps scientists extract useful quantitative information about a sample's chemical composition or electronic structure. To make this process more efficient, we have developed a new open-source software tool called SpectraFit. This tool allows users to perform quick data fitting using expressions of distribution and linear functions through the command line interface (CLI) or Jupyter Notebook, which can run on Linux, Windows, and MacOS, as well as in a Docker container. As part of our commitment to good scientific practice, we have introduced an output file-locking system to ensure the accuracy and consistency of information. This system collects input data, results data, and the initial fitting model in a single file, promoting transparency, reproducibility, collaboration, and innovation. To demonstrate SpectraFit's user-friendly interface and the advantages of its output file-locking system, we are focusing on a series of previously published iron-sulfur dimers and their XAS spectra. We will show how to analyze the XAS spectra via CLI and in a Jupyter Notebook by simultaneously fitting multiple data sets using SpectraFit. Additionally, we will demonstrate how SpectraFit can be used as a black box and white box solution, allowing users to apply their own algorithms to engineer the data further. This publication, along with its Supporting Information and the Jupyter Notebook, serves as a tutorial to guide users through each step of the process. SpectraFit will streamline the peak fitting process and provide a convenient, standardized platform for users to share fitting models, which we hope will improve transparency and reproducibility in the field of spectroscopy.

Preparation of Carbon-Based Solid Acid Catalyst from High-Sulfur Petroleum Coke with Nitric Acid and Ball Milling, and a Computational Evaluation of Inherent Sulfur Conversion Pathways.

A series of petroleum coke (petcoke)-derived solid acid catalysts were prepared via nitric acid treatment with or without ball milling pretreatment. The inherent sulfur in petcoke was converted to sulfonic groups, which were active sites for the esterification of octanoic acid and methanol at 60 °C, with ester yields of 14-43%. More specifically, samples without ball milling treated at 120 °C for 3 h had a total acidity of 4.67 mmol/g, which was 1.6 times that of the samples treated at 80 °C, despite their -SO3H acidities being similar (~0.08 mmol/g). The samples treated for 24 h had higher -SO3H (0.10 mmol/g) and total acidity (5.25 mmol/g) but not increased catalytic activity. Ball milling increased the defects and exposed aromatic hydrogen groups on petcoke, which facilitated further acid oxidation (0.12 mmol -SO3H/g for both materials and total acidity of 5.18 mmol/g and 5.01 mmol/g for BP-N-3/120 and BP-N-8/90, respectively) and an increased ester yield. DFT calculations were used to analyze the pathways of sulfonic acid group formation, and the reaction pathway with NO2• was the most thermodynamically and kinetically favourable. The activities of the prepared catalysts were related to the number of -SO3H acid sites, the total acidity, and the oxygen content, with the latter two factors having a negative impact.

Catalytic activation via π-backbonding in halogen bonds.

The role of halogen bonding (XB) in chemical catalysis has largely involved using XB donors as Lewis acid activators to modulate the reactivity of partner Lewis bases. We explore a more uncommon scenario, where a Lewis base modulates reactivity via a spectator halogen bond interaction. Our computational studies reveal that spectator halogen bonds may play an important role in modulating the rate of SN2 reactions. Most notably, π acceptors such as PF3 significantly decrease the barrier to substitution by decreasing electron density in the very electron rich transition state. Such π-backbonding represents an example of a heretofore unexplored situation in halogen bonding: the combination of both σ-donation and π-backdonation in this "non-covalent" interaction. The broader implications of this observation are discussed.

CBD hydroxyquinone photo-isomerises to a highly reactive intermediate.

The legalisation of hemp has led to wide commercial availability of cannabidiol (CBD)-containing products. Here we show that the CBD-hydroxyquinone (HU-331), a readily formed oxidation product and common impurity in CBD isolates, undergoes a previously unknown photo-isomerisation to produce a highly reactive intermediate in solution. Studies supported by calculations indicate that this intermediate rapidly reacts with oxygen to form a multitude of cannabinoid products. The purple colour observed in light-aged CBD-containing solutions is largely due to the anions of these by-products and is not significantly due to the HU-331 anion. Our findings suggest that these uncharacterized cannabinoid derivatives can be present in CBD-containing e-liquids and solutions that have been stored under ambient light conditions, calling for quality control processes that manage HU-331 contamination.

Reaction of 3-Cl/OMe-Substituted 5-Nitrobenzisothiazoles with Hydrazine: Structural and Computational Evidence for Rearrangement Pathways Implicating Intramolecular Formation of Pivotal Meisenheimer Complexes.

In projected structure-activity relationship studies of the novel diheteroarylamide-based anti-HIV agent 2 (1C8), one objective was to evaluate the influence of incorporating the central amide motif in 2 into a five-membered pyrazolone ring, as found in 3. It was envisaged that compound 3 could be prepared through reaction of 3-hydrazino-5-nitrobenzisothiazole 5 with the methyl ester of 4-chloropyridine-3-carboxylic acid, followed by N-methylation of the pyridine nitrogen. However, the reaction of 3-methoxyl-5-nitrobenzisothiazole with hydrazine resulted in formation of ring-opened hydrazonate product 18. In the corresponding reaction with 3-chloro-5-nitrobenzisothiazole, a different rearrangement product 19 was formed, in which two 2,1-benzisothiazole units are joined by a sulfur bridge. Meisenheimer complex formation, favored by the presence of the 5-nitro substituent on the benzisothiazole ring, was postulated to be a key feature in the formation of these deep-seated rearrangement products. Support for the proposed formation of the pivotal Meisenheimer complexes and their subsequent evolution to the observed products in which the benzisothiazole sulfur atom is either expelled or maintained in the isomeric 2,1-benzisothiazole system was obtained by density function theory calculations.

Nature of S-N Bonding in Sulfonamides and Related Compounds: Insights into π-Bonding Contributions from Sulfur K-Edge X-ray Absorption Spectroscopy.

Molecules containing sulfur-nitrogen bonds, like sulfonamides, have long been of interest because of their many uses and interesting chemical properties. Understanding the factors that cause sulfonamide reactivity is important, yet there continues to be controversy regarding the relevance of S-N π bonding in describing these species. In this paper, we use sulfur K-edge X-ray absorption spectroscopy (XAS) in conjunction with density functional theory (DFT) to investigate the role of S3p contributions to π-bonding in sulfonamides, sulfinamides, and sulfenamides. We explore the nature of the electron distribution of the sulfur atom to its nearest neighbors and widen our scope to its effects on rotational barriers along the sulfur-nitrogen axis. The experimental XAS data together with time-dependent DFT calculations confirm that sulfonamides-and the other sulfinated amides in this series-have essentially no S-N π bonding involving S3p contributions and that electron repulsion is the dominant force affecting rotational barriers along the S-N axis.

Direct metal-carbon bonding in symmetric bis(C-H) agostic nickel(i) complexes.

Agostic interactions are examples of σ-type interactions, typically resulting from interactions between C-H σ-bonds with empty transition metal d orbitals. Such interactions often reflect the first step in transition metal-catalysed C-H activation processes and thus are of critical importance in understanding and controlling σ bond activation chemistries. Herein, we report on the unusual electronic structure of linear electron-rich d9 Ni(i) complexes with symmetric bis(C-H) agostic interactions. A combination of Ni K edge and L edge XAS with supporting TD-DFT/DFT calculations reveals an unconventional covalent agostic interaction with limited contributions from the valence Ni 3d orbitals. The agostic interaction is driven via the empty Ni 4p orbitals. The surprisingly strong Ni 4p-derived agostic interaction is dominated by σ contributions with minor π contributions. The resulting ligand-metal donation occurs directly along the C-Ni bond axis, reflecting a novel mode of bis-agostic bonding.

Five Nitrogen Oxidation States from Nitro to Amine: Stabilization and Reactivity of a Metastable Arylhydroxylamine Complex.

Redox noninnocent ligands enhance the reactivity of the metal they complex, a strategy used by metalloenzymes and in catalysis. Herein, we report a series of copper complexes with the same ligand framework, but with a pendant nitrogen group that spans five different redox states between nitro and amine. Of particular interest is the synthesis of a unprecedented copper(I)-arylhydroxylamine complex. While hydroxylamines typically disproportionate or decompose in the presence of transition metal ions, the reactivity of this metastable species is arrested by the presence of an intramolecular hydrogen bond. Two-electron oxidation yields a copper(II)-(arylnitrosyl radical) complex that can dissociate to a copper(I) species with uncoordinated arylnitroso. This combination of ligand redox noninnocence and hemilability provides opportunities in catalysis for two-electron chemistry via a one-electron copper(I/II) shuttle, as exemplified with an aerobic alcohol oxidation.

π covalency in the halogen bond.

Halogen bonds are a highly directional class of intermolecular interactions widely employed in chemistry and chemical biology. This linear interaction is commonly viewed to be analogous to the hydrogen bond because hydrogen bonding models also intuitively describe the σ-symmetric component of halogen bonding. The possibility of π-covalency in a halogen bond is not contemplated in any known models. Here we present evidence of π-covalency being operative in halogen bonds formed between chloride and halogenated triphenylamine-based radical cations. We reach this conclusion through computational analysis of chlorine K-edge X-ray absorption spectra recorded on these halogen bonded pairs. In light of this result, we contend that halogen bonding is better described by analogy to metal coordination bonds rather than hydrogen bonds. Our revised description of the halogen bond suggests that these interactions could be employed to influence the electronic properties of conjugated molecules in unique ways.

Direct experimental evaluation of ligand-induced backbonding in nickel metallacyclic complexes.

The details of ligand-induced backbonding in nickel diphosphine π complexes are explored using nickel L-edge (3d←2p) X-ray absorption spectroscopy as a means of quantifying the degree of backbonding derived from direct Ni 3d donation into the π ligand. It is observed that backbonding into weakly π acidic ligands such as alkenes and arenes is dominated by contributions from the diphosphine ligand via σ-donation, leading to activated metallacycles with a Ni(0) d10 metal centre. With more strongly π acidic ligands, however, metal contributions to backbonding increase substantially leading to a more electron-deficient metal centre that is best described as having a Ni(i) spectroscopic oxidation state.

The Importance of Ligand-Induced Backdonation in the Stabilization of Square Planar d10 Nickel π-Complexes.

The electronic nature of Ni π-complexes is underexplored even though these complexes have been widely postulated as intermediates in organometallic chemistry. Herein, the geometric and electronic structure of a series of nickel π-complexes, Ni(dtbpe)(X) (dtbpe=1,2-bis(di-tert-butyl)phosphinoethane; X=alkene or carbonyl containing π-ligands), is probed using a combination of 31 P NMR, Ni K-edge XAS, Ni Kß XES, and DFT calculations. These complexes are best described as square planar d10 complexes with π-backbonding acting as the dominant contributor to M-L bonding to the π-ligand. The degree of backbonding correlates with 2 JPP from NMR and the energy of the Ni 1s→4pz pre-edge in the Ni K-edge XAS data, and is determined by the energy of the π*ip ligand acceptor orbital. Thus, unactivated olefinic ligands tend to be poor π-acids whereas ketones, aldehydes, and esters allow for greater backbonding. However, backbonding is still significant even in cases in which metal contributions are minor. In such cases, backbonding is dominated by charge donation from the diphosphine, which allows for strong backdonation, although the metal centre retains a formal d10 electronic configuration. This ligand-induced backbonding can be formally described as a 3-centre-4-electron (3c-4e) interaction, in which the nickel centre mediates charge transfer from the phosphine σ-donors to the π*ip ligand acceptor orbital. The implications of this bonding motif are described with respect to both structure and reactivity.

Regiocontrolled and Stereoselective Syntheses of Tetrahydrophthalazine Derivatives using Radical Cyclizations.

Tetrahydrophthalazine derivatives have found important applications in pharmaceutical research, but existing synthetic methods are unable to access them regio- and stereoselectively. Here, a new approach is presented that addresses these challenges by utilizing a 6-endo-trig radical cyclization in the key step. The desired tetrahydrophthalazines can be accessed in high yields (55-98 %) and high diastereoselectivities for the trans-product (>95:5) starting either from readily accessible hydrazones, or from the corresponding aldehydes and substituted Boc-hydrazides in a one-pot process. The synthetic versatility of the tetrahydrophthalazine core was demonstrated by its straightforward conversion to dihydro-phthalazines, phthalazines, or pyrazolo dione derivatives. Furthermore, the N-N bond was reduced to afford a new route to 1,4-diamines.

Anthracene as a Launchpad for a Phosphinidene Sulfide and for Generation of a Phosphorus-Sulfur Material Having the Composition P2S, a Vulcanized Red Phosphorus That Is Yellow.

Thermolysis of a pair of dibenzo-7-phosphanorbornadiene compounds is shown to lead to differing behaviors: phosphinidene sulfide release and formation of amorphous P2S. These compounds, tBuP(S)A (1, A = C14H10 or anthracene; 59% isol. yield) and HP(S)A (2; 63%), are available through thionation of tBuPA and the new secondary phosphine HPA (5), prepared from Me2NPA and DIBAL-H in 50% yield. Phosphinidene sulfide [ tBuP═S] transfer is shown to proceed efficiently from 1 to 2,3-dimethyl-1,3-butadiene to form Diels-Alder product 3 with a zero-order dependence on diene. Platinum complex (Ph3P)2Pt(η2- tBuPS) (4, 47%) is also accessed from 1 and structurally characterized. In contrast, heating parent species 2 (3 h, 135 °C) under vacuum instead produces an insoluble, nonvolatile yellow residual material 6 of composition P2S that displays semiconductor properties with an optical band gap of 2.4 eV. Material 6 obtained in this manner from molecular precursor 2 is in a poorly characterized portion of the phosphorus-sulfur phase diagram and has therefore been subjected to a range of spectroscopic techniques to gain structural insight. X-ray spectroscopic and diffraction techniques, including Raman, XANES, EXAFS, and PDF, reveal 6 to have similarities with related compounds including P4S3, Hittorf's violet phosphorus. Various possible structures have been explored as well using quantum chemical calculations under the constraint that each phosphorus atom is trivalent with no terminal sulfide groups, and each sulfur atom is divalent. The structural conclusions are supported by data from phosphorus-31 magic angle spinning (MAS) solid state NMR spectroscopy, bolstering the structural comparisons to other phosphorus-sulfur systems while excluding the formulation of P2S as a simple mixture of P4S3 and phosphorus.

Identifying the missing link in catalyst transfer polymerization.

Nickel-catalyzed catalyst transfer polycondensation (CTP) of thiophenes is an efficient strategy for the controlled synthesis of polythiophenes. However, a detailed view of its reaction mechanism has remained elusive with unresolved questions regarding the geometry and bonding of critical Ni(0) thiophene intermediates. Herein, we provide experimental and computational evidence of structurally characterized square planar η2-Ni(0)-thiophene species and their relevance to the mechanism of CTP. These results confirm the viability of C,C-η2 bound intermediates in CTP of thiophenes, providing an electronic rationale for the stability of such species, and thus that such processes can proceed as living polymerizations. We further show that C,S-κ2 species may also be relevant in nickel-catalyzed CTP of thiophenes, providing new avenues for exploitation and optimization.