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Pressures on freshwater biodiversity in Southeast Asia are accelerating, yet the status and conservation needs of many of the region’s iconic fish species are poorly known. The Mekong is highly species diverse and supports four of the six largest freshwater fish globally, three of which, including Mekong giant catfish (Pangasianodon gigas), are Critically Endangered. Emerging environmental DNA (eDNA) techniques have potential for monitoring threatened freshwater biodiversity, yet have not been applied in complex and biodiverse tropical ecosystems such as the Mekong. We developed species-specific primers for amplifying Mekong giant catfish DNA. In situ validation demonstrated that the DNA amplification was successful for all samples taken in reservoirs with known presence of Mekong giant catfish independent of fish density. We collected water samples from six deep pools on the Mekong, identified through Local Ecological Knowledge, in Cambodia, Lao PDR, and Thailand. DNA was extracted and amplified from these samples using the designed primers and probes. Mekong giant catfish DNA was detected from one sample from the species’ presumed spawning grounds on the Mekong mainstream, near the border between northern Thailand and Lao PDR. eDNA sampling using species-specific primers has potential for surveying and monitoring poorly known species from complex tropical aquatic environments. However accounting for false absences is likely to be required for the method to function with precision when applied to extremely rare species that are highly dispersed within a large river system. We recommend that such approach be utilised more widely by freshwater conservation practitioners for specific applications. The method is best suited for baseline biodiversity assessments or to identify and prioritise locations for more rigorous sampling. Our methods are particularly relevant for systems or species with limited baseline data or with physical characteristics that logistically limit the application of conventional methods. Such attributes are typical of large tropical rivers such as the Mekong, Congo, or Amazon.

A borazine derivative functionalized by nitroxide free radicals, N , N ', N ″-(tris(4-Bromophenyl))- B , B ', B ″-tris((2,6-dimethyl-4-( N - tert -butyl- N -oxyamino)phenyl) borazine ( TriBNit ), was synthesized as a milestone of open-shell inorganic benzene. The crystal structure determined from X-ray diffraction on a single crystal ascertains the grafting of three nitroxide radicals. The temperature dependence of the magnetic susceptibility evidences weak intramolecular antiferromagnetic interactions between the radicals with strong intermolecular antiferromagnetic interactions between two nitroxide moieties of two neighboring molecules. EPR spectroscopy at 80 K on a frozen glassy solution evidences the coexistence of S = 1/2 and S = 3/2 ground-spin state species. This is ascribed to the nitroxide radicals having different orientations with respect to the borazine core giving rise either to antiferromagnetic interaction with a low ground-spin state S = 1/2 or to ferromagnetic interaction with a high ground-spin state S = 3/2 as supported by theoretical data. At room temperature, because of nitroxide mobility, the EPR spectrum is averaged to a ground-spin state S = 1/2.

This publication aims at presenting a Python-based workflow designed to enable a fully automatised and exhaustive exploration of the conformational degrees of freedom within the calculation of reaction paths in molecular systems. The proposed strategy focuses on effectively representing the lowest energy conformers for intricate, highly rotatable, and non-intuitive transition states, reagents and products, using existing computational tools. The article presents a workflow that is demonstrated through the application of five chemical reactions, chosen to be representative of the diversity and complexity of actual experimental studies, and which often prove to be challenging to study "by hand". The proposed methodology is expected to be of a great help in the modelling of state-of-the art organic chemistry reactions, whose complexity is ever increasing.

Electrophilic aromatic substitution is one of the most mechanistically studied reactions in organic chemistry. However, precluded by innate substituent effects, the access to certain substitution patterns remains elusive. While selective C-H alkylation of biorelevant molecules is eagerly awaited, especially for the insertion of a methyl group whose magic effect can boost lead molecules potency, one of the most obvious strategies would rely on electrophilic aromatic substitution. Yet, the historical Friedel-Crafts methylation remains to date poorly selective and limited to activated simple aromatics. Here, we report the development of a selective electrophilic methylation enabling the direct access to highly desirable 1,3-disubstituted arenes. This study demonstrates that this reaction is driven by the generation of long-lived arenium intermediates generated by protonation in superacid and can be applied to a large variety of functionalized (hetero)aromatics going from standard building blocks to active pharmaceutical ingredients., (© 2024. The Author(s).)

Context: In this article, we adapt a recent proposition to use a Fermi-Dirac-type population scheme on Kohn-Sham molecular orbitals to the case of an interaction with a thermalised electrode. This allows to derive a fundamental non-linear equation linking the chemical potential of the electrode and the amount of charge transferred to the system under study, hence allows to quantify the propensity to charge transfer (philicity). This methodology is applied to a large set of common electrophiles and nucleophiles, showing decent relation with more standard philicity descriptors. Chemical hardness is also revisited by this approach., Methods: All calculations were performed using the Gaussian 16 software package at the M062X/aug-cc-pvtz level of theory. Data analysis was then performed through a Python3 dedicated program (relying on the fsolve numerical solver from the SciPy package), using Gaussian output files, and available as supplementary material., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

An original concerted antarafacial mechanism for the addition of diorganosilyl-zinc reagents across the C-C triple bond of ynamides is computationally investigated using DFT calculations. This concerted mechanism, leading to a trans-product in only one step, results in the formation of a Si-C and a Zn-C σ-bond on opposite sides of the π-system. We demonstrate that the mechanism going through a η 2 -vinyl intermediate and the proposal of a radical chain pathway are energetically unsustainable. The retained concerted antarafacial pathway is tested on experimental selectivities: the regioselectivity, in favor of the silyl β-addition in ynamide, and stereoselectivity, which is cis- with (Me 2 PhSi) 2 Zn but trans- with [(Me 3 Si) 3 Si] 2 Zn, are well reproduced by DFT calculations. The regio- and stereoselectivity are discussed using the activation strain model and a chemical bonding analysis., (© 2024 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Conceptual density functional theory (CDFT) and the quantum reactivity descriptors stemming from it have proven to be valuable tools for understanding the chemical behavior of molecules. This article is presented as being intrinsically of dual character. In a first part, it briefly reviews, in a deliberately didactical way, the main ensembles in CDFT, while the second half presents two additional ensembles, where the chemical hardness acts as a natural variable, and their respective reactivity descriptors. The evaluation of these reactivity descriptors on common organic chemical reagents are presented and discussed., (© 2024 Wiley Periodicals LLC.)

The accumulation of chiral ammonium-oxocarbenium dications in superacid is evidenced by low-temperature NMR spectroscopy, X-ray diffraction analysis and confirmed by DFT calculations. Its potential for the diastereoselective remote hydrofunctionalization of non-activated alkene is also explored., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

In this study, first-principles calculations were employed to rationally design two-dimensional (2D) Janus transition metal nitrides of P 3 m 1 M 2 N 3 phases, where M is a d-block element (Sc-Zn, Y-Cd, Hf-Hg). Among the 29 examined 2D M 2 N 3 , three 2D phases, namely P 3 m 1 Cu 2 N 3 , Zr 2 N 3 , and Hf 2 N 3 , exhibit excellent thermodynamic, dynamic, mechanical, and thermal stabilities. These novel Janus 2D materials exhibit ferromagnetic metallic and half-metallic behavior. The related 2D Janus surface-functionalized derivatives, Cu 2 N 3 H, Cu 2 N 3 F, Cu 2 N 3 Cl, Zr 2 N 3 H, Hf 2 N 3 H, and Hf 2 N 3 F, are all dynamically stable. The 2D Janus P 3 m 1 phases of Zr 2 N 3 H, Hf 2 N 3 H, and Hf 2 N 3 F, all with M in the +IV oxidation state, act as semiconductors in the visible region, with energy band gaps of 2.26-2.70 eV at the HSE06 level of theory. On the other hand, the 2D Janus P 3 m 1 Cu 2 N 3 X phases (where X = H, F, and Cl) are ferromagnetic half-metals. Additionally, it has been unveiled that there are high hole mobilities (∼6 × 10 3 cm 2 V -1 s -1 ) derived from the moderate deformation potential and effective mass in the 2D Janus P 3 m 1 Zr 2 N 3 H, Hf 2 N 3 H, and Hf 2 N 3 F phases. Uniaxial strain engineering has demonstrated the outstanding in-plane piezoelectric properties of 2D Janus P 3 m 1 Zr 2 N 3 H, Hf 2 N 3 H, and Hf 2 N 3 F with high d 11 values (∼99.91 pm V -1 ). Furthermore, the desirable band-edge alignments and high anisotropic carrier mobilities of 2D Janus P 3 m 1 Zr 2 N 3 H, Hf 2 N 3 H, and Hf 2 F phases indicate their potential as visible light-driven photocatalysts for water splitting reactions on different facets. These properties render 2D Janus 3 F phases indicate their potential as visible light-driven photocatalysts for water splitting reactions on different facets. These properties render 2D Janus P 3 m 1 Zr 2 N 3 H, Hf 2 N 3 H, and Hf 2 F phases promising for use in optoelectronics, piezoelectric sensing, and photocatalysis applications.3 F phases promising for use in optoelectronics, piezoelectric sensing, and photocatalysis applications.

Furfural is an industrially relevant biobased chemical platform. Unlike classical furan, or C-alkylated furans, which have been previously described in the current literature, the =C 5 H bond of furfural is unreactive. As a result, on a large scale, C=C and C=O bond hydrogenation/hydrogenolysis is mainly performed, with furfuryl alcohol and methyl tetrahydrofuran being the two main downstream chemicals. Here, we show that the derivatization of the -CHO group of furfural restores the reactivity of its =C 5 H bond, thus permitting its double condensation on various alkyl aldehydes. Overcoming the recalcitrance of the =C 5 H bond of furfural has opened an access to a biobased monomer, whose potential have been investigated in the fabrication of renewably-sourced poly(silylether). By means of a combined theoretical-experimental study, a reactivity scale for furfural and its protected derivatives against carbonylated compounds has been established using an electrophilicity descriptor, a means to predict the molecular diversity and complexity this pathway may support, and also to de-risk any project related to this topic. Finally, by using performance criteria for industrial operations in the field of fuels and commodities, we discussed the industrial potential of this work in terms of cost, E-factor, reactor productivity and catalyst consumption., (© 2024 The Authors. ChemSusChem published by Wiley-VCH GmbH.)

Harnessing the acidity of HF/base reagents is of paramount importance to improve the efficiency and selectivity of fluorination reactions. Yet, no general method has been reported to evaluate their acidic properties, and experimental designs are still relying on a trial-and-error approach. We report a new method based on 19 F NMR spectroscopy which allows highly sensitive measures and short-time analyses. Advantageously, the basic properties of the indicators can be determined upstream by DFT calculations, affording a simple yet robust semiempirical approach. In particular, the indicators used in this study were rationally designed to fit on the conceptually appealing and commonly used Hammett scale. This method has been applied to commercially available and recently developed HF/base reagents.

In this study, we investigate the potential of the 18-crown-6-like two-dimensional (2D)-N 8 structure to accommodate electrons from metals without compromising its covalent nitrogen network. Employing the crystal structure prediction enhanced by evolutionary algorithm and density functional theory methodology, we successfully predicted the existence of 16 layered M@2D-N 8 complexes from a total of 39 MN 8 systems investigated at 100 GPa (M = s-block Na-Cs, Be-Ba and d-block Ag, Au, Cd, Hg, Hf, W, and Y). Among those, there are 13 quenchable M@2D-N 8 compounds that are dynamically stable at 1 atm. Orbital interactions and bonding analysis show that 2D-N 8 presents a flat localized π* band that can accommodate one or two electrons without breaking the 2D covalent nitrogen network. Depending on the metal-to-polynitrogen charge transfer (formally, 1-4 electrons), these N-rich phases are semiconducting or metallic under ambient conditions. Ab initio molecular dynamics simulations show that K(I)@2D-N 8 and Ca(II)@2D-N 8 are thermally stable up to 600 K, while the Hf(IV)@2D-N 8 compound is thermally not viable at 400 K because of the weakening of the N═N bonds due to a strong four-electron reduction. These metal 18-crown-6 ring-based polynitrogen compounds, as expected due to their high nitrogen content (eight nitrogen atoms per metal), could potentially serve as new high-energy density materials.

Here we report a method to reorganize the core structure of aliphatic unsaturated nitrogen-containing substrates exploiting polyprotonation in superacid solutions. The superelectrophilic activation of N-isopropyl systems allows for the selective formal C sp3 -H activation/cyclization or homologation / functionalization of nitrogen-containing substrates. This study also reveals that this skeletal reorganization can be controlled through protonation interplay. The mechanism of this process involves an original sequence of C-N bond cleavage, isopropyl cation generation and subsequent C-N bond and C-C bond formation. This was demonstrated through in situ NMR analysis and labelling experiments, also confirmed by DFT calculations., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

In the present study, ab initio evolutionary algorithms and heuristic approach were used to predict new two-dimensional (2D) hydrogen cyanide crystalline phases based on HCN and HNC molecular building blocks. Our research revealed thirty-seven 2D HCN and HNC structures within six topological families which contain N 1 , N 2 dimers, N 3 trimers, infinite poly-N motifs, or zigzag C-C chains. HSE06 functional calculations indicated that 2D 1 Pmn 2 1 HCN, 2 Pma 2 HCN, 3 P 2 1 2 1 2 HCN, and 6 Pbcm HNC are direct semiconductors with band gaps E of 5.1, 4.2, 4.3, and 2.8 eV, respectively, and isovalent element substitutions (C by Ge/Si, and H by F) were performed to tune the electronic band gaps of the resulting 2D structures ( g of 5.1, 4.2, 4.3, and 2.8 eV, respectively, and isovalent element substitutions (C by Ge/Si, and H by F) were performed to tune the electronic band gaps of the resulting 2D structures ( E g = 1.2-7.4 eV). Moreover, it has been found that the high in-plane Young's modulus (330.3-445.8 N m -1 ) and strong tolerance of direct band transitions ( E g = 1.2-5.3 eV) against the external biaxial strains in these four 2D HCN structures endow them with potential applications in photofunctional and flexible electronic devices. Finally, ab initio molecular dynamics simulations showed that at 50 GPa and 400 K, HCN molecules in a bulk I 4 mm hydrogen cyanide molecular crystal can extend to 2D HCN covalent nets.

In this work, we unveiled a new class of two-dimensional (2D) group IV nitride A x N y (A = Sn, Ge, or Si) prototypes, C 2/ m A 4 N, P 3̅ m 1 A 3 N, P 3 m 1 A 2 N, P 3̅ m 1 A 3 N 2 , P 6̅ m 2 AN, P 3̅ m 1 AN, P 6̅2 m A 3 N 4 , P 3 m 1 A 2 N 3 , P 4̅2 1 m AN 2 , and P 3̅ m 1 AN 3 , by using evolutionary algorithms combined with first-principles calculations. Using HSE06 functional calculations, a wide range of band gaps from metal to semiconductor (0.405-5.050 eV) and ultrahigh carrier mobilities (1-24 × 10 3 cm 2 V -1 s -1 ) were evidenced in these 2D structures. We found that 2D P 3 m 1 Sn 2 N 3 , Ge 2 N 3 , and Si 2 N 3 are intrinsic ferromagnetic semiconductors with gaps of 0.677, 1.285, and 2.321 eV, respectively. The lattice symmetry and Si-to-N 2 charge transfer upon strain lead to large anisotropic negative Poisson's ratios (-0.281 to -0.146) along whole in-plane directions in 2D P 4̅2 1 m SiN 2 . Our findings not only enrich the family of 2D nitrides but also highlight the promising optoelectronic and nanoauxetic applications of 2D group IV nitrides.

Mechanistic details of cellulose depolymerization by non-thermal (atmospheric) plasma (NTAP) remains under-explored given the complexity of the medium. In this study, we have investigated the reaction mechanism of glycosidic-bond degradation triggered by reaction with hydroxyl radicals, considered as the principal reactive species in NTAP medium. In the first step of reaction sequence, H-abstraction reactions by HO ‧ . radical on different CH sites of the pyranose ring were found to be non-selective and markedly exergonic giving rise to a set of cellobiosyl carboradicals likely to undergo further reactions. We then showed that cellobiosyl carboradicals are protected against direct hydrolysis, no activation of the (1-4)- β -glycosidic bond being characterized. Interestingly, a simple homolytic bond cleavage allowed to obtain desired monomer. Among the 18 possible fragmentations, involving CC and CO bond breaking from cellobiosyl carboradicals, 14 transition states were successfully identified, and only three reaction pathways proved kinetically and thermodynamically feasible. Natural bond orbital (NBO) analysis was performed to shed light on electronic structures of different compounds., (© 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.)

Enantioenriched complex fused-tricyclic azepanes or bridged-polycyclic azocanes were constructed via a two-step sequence involving an enantioselective organocascade followed by superacid activation of the domino adduct. The activated oxa-bridged azepane acts as a key hidden heptacyclic chiral N-acyl iminium ion triggering a chemo- and diastereoselective intramolecular mono- or di-arylation., (© 2022 Wiley-VCH GmbH.)

Electronic effects (inductive and mesomeric) are of fundamental importance to understand the reactivity and selectivity of a molecule. In this article, polarisation temperature is used as a principal index to describe how electronic effects propagate in halogeno-alkanes and halogeno-alkenes. It is found that as chain length increases, polarisation temperature decreases. As expected, polarisation is much larger for alkenes than for alkanes. Finally, the polarisation mode of the carbon-fluorine bond is found to be quite different and might explain the unusual reactivity of fluoride compounds.

In this study, the ternary phase diagram of the Tc-Al-B system is constructed by a combination of an evolutionary algorithm and density functional theory calculations. Four novel phases are predicted, including three binary compounds ( P 1̄ Al 7 B 15 , Cmcm TcAl 2 , and C 2 TcAl 3 ) and one ternary compound ( Cmmm Tc 2 AlB 2 ). All predicted structures are mechanically, dynamically, and thermodynamically stable. Among the predicted phases, P 1̄ Al 7 B 15 resembles the experimental structure of Al 0.93 B 2 and Cmmm Tc 2 AlB 2 corresponds to the 212-type MAB phase. Due to the in- and out-of-plane anisotropic chemical bonding in Cmmm Tc 2 AlB 2 , a tetragonal two-dimensional (2D) Tc 2 B 2 structure could be possibly exfoliated by chemical removal of Al atoms. The electronic structure calculations indicate that the 2D Tc 2 B 2 structure and its potential layered precursors are all metallic. Furthermore, the chemical reactivity of H, F, O and, OH ligands with the 2D Tc 2 B 2 surface is studied and the associated 2D surface-functionalized Tc 2 B 2 derivatives are found to be metallic. It is revealed that the F and O functional groups strengthen the surface atomic layer of 2D Tc 2 B 2 and enhance the Young's moduli.

In the present work, three new semiconducting two-dimensional (2D) Te phases containing three- and four-coordinated Te centers were proposed by using evolutionary algorithms combined with first-principles calculations. Using density functional theory calculations, we discussed the bonding and electronic properties in these phases, and subsequently rationalized their structures. The viability of these predicted structures was demonstrated by evaluating their thermodynamic, dynamic, mechanical, and thermal stabilities. Moreover, a significant direct band gap (0.951-1.512 eV) and excellent transport properties were evidenced in 2D Te nets, which suggests that they could be promising photovoltaic materials candidates. This is further supported by the stability of the associated bulk layered counterparts of the 2D Te nets., Competing Interests: There is no conflict of the interest among the authors., (This journal is © The Royal Society of Chemistry.)

The present work reports the computational study of the major Diels-Alder reaction between 2-bromocycloalkenone and a variety of mono- and di-substituted dienes. Through density functional theory (DFT) calculations and subsequent activation strain model/energy decomposition analysis/conceptual DFT (C-DFT) analyses, the key factors governing the activation barriers heights, and thus reactivity, are characterized. In contrast with a previous study, steric effects do not appear to control reactivity. Conversely, in all presented cases, a subtle interplay between deformation and interaction energies is evidenced at transition states. In the end, neither term alone is enough to explain or predict reactivity. Yet a simple C-DFT descriptor allows to predict with a reasonable efficiency the activation barriers: the excitation energy needed to observe a charge transfer from the diene to the dienophile. Theoretical elements are provided to support the use of this descriptor., (© 2021 Wiley Periodicals LLC.)

The synthesis of relevant renewable aromatics from bio-based furfural derivatives and cheap alkenes is carried out by using a Diels-Alder/aromatization sequence. The prediction and the control of the ortho/meta selectivity in the Diels-Alder step is an important issue to pave the way to a wide range of renewable aromatics, but it remains a challenging task. A combined experimental-theoretical approach reveals that, as a general trend, ortho and meta cycloadducts are the kinetic and thermodynamic products, respectively. The nature of substituents, both on the dienes and dienophiles, significantly impacts the feasibility of the reaction, through a modulation on the nucleo- and electrophilicity of the reagents, as well as the ortho/meta ratio. We show that the ortho/meta selectivity at the reaction equilibrium stems from a subtle interplay between charge interactions, favoring the ortho products, and steric interactions, favoring the meta isomers. This work also points towards a path to optimize the aromatization step., (© 2020 Wiley-VCH GmbH.)

A fundamental link between conceptual density functional theory and statistical thermodynamics is herein drawn, showing that intermolecular electrostatic interactions can be understood in terms of effective work and heat exchange. From a more detailed analysis of the heat exchange in a perturbation theory framework, an associated entropy can be subsequently derived, which appears to be a suitable descriptor for the local polarisability of the electron density. A general rule of thumb is evidenced: the more the perturbation can be spread, both through space and among the excited states, the larger the heat exchange and entropy.

The never-elucidated crystal structure of metastable iron disulfide FeS 2 resulting from the full deintercalation of Li in Li 2 FeS 2 has been cracked thanks to crystal structure prediction searches based on an evolutionary algorithm combined with first-principles calculations accounting for experimental observations. Besides the newly layered C 2/ m polymorph of iron disulfide, two-dimensional dynamically stable FeS 2 phases are proposed that contain sulfides and/or persulfide S 2 motifs.

In this paper, we show that trans effects in octahedral complexes can primarily be related to differences in the ability, for a given ligand, to cede electron density to the metal cation under the influence of the ligand at the trans position. Using tools from conceptual DFT or from related paradigms, we highlight these effects on a set of representative examples and further provide the basis for a computational trans effect scale. This quantification notably retrieves the experimental trans orienting series.

A large up-field shift (-763 ppm) has been observed for the carboxyl carbons of the dichlorido complex TBA[Ru(2)(O(2)CCH(3))(4)Cl(2)] (TBA(+) = tetra(n-butyl)ammonium cation) in the (13)C NMR spectrum (CD(2)Cl(2) at 25 °C). The DFT calculations showed spin delocalization from the paramagnetic Ru(2)(5+) core to the ligands, in agreement with the large up-field shift.

The electrophilicity index, μ(2)/2η, where μ is the chemical potential and η is the hardness, has been defined by Parr, Von Szentpaly, and Liu (J. Am. Chem. Soc., 1999, 121, 1922) as the lowering in energy of an electronic system during a process in which the chemical potential of the system raises from μ to zero, accepting -μ/η electrons. In this work, it is shown that the electrophilicity index is also a rational choice for measuring nucleophilicity. Indeed, within the grand canonical ensemble, when the chemical potential of a system increases from μ to zero, the system gives away μ/η electrons. During the process, the variation of the grand potential is μ(2)/2η. Additionally, through the use of a second order Taylor series expansion of the density as a function of the number of electrons, at constant external potential, which depends on the Fukui function and the dual descriptor, the local electrophilicity is defined as the actual variation of the electron density when the system acquires -μ/η electrons, while the local nucleophilicity is similarly defined for the case when the system loses μ/η electrons.

In this paper, we show that the ambiphilic properties of some organic ligands in organometallic complexes may be retrieved readily from simple calculations in the framework of conceptual density functional theory (C-DFT): namely, the dual descriptor (DD) and the molecular electrostatic potential (MEP) of the ligands afford a rather straightforward interpretation of experimental trends such as the bonding geometry and the electronic properties of complexes in terms of σ-, π- and back-bonding. The studied ligands were chosen to be representative of the wide variety organometallic chemistry offers, ranging from neutral to charged systems and from diatomic to polyatomic molecules. The present approach is general since all relevant parameters are retrieved from the electron density, obtained either from a DFT or post-Hartree-Fock calculation. It is believed to be helpful for organometallic chemists, since it allows a deep understanding and may be used as a predictive tool of the coordinating properties of ligands.