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The catalytic effect of Si‐doped graphene nanoflakes (NFs) on CO2 reduction with molecular hydrogen was explored theoretically at the TPSS/def2‐SVP+D3BJ level of theory. Substituting carbon with silicon generates defects in the NF structure, which leads to a polyradical ground state of the NF. The silicon defect enhances the reactivity towards the substrates. Si‐doped graphene NFs exhibit higher catalytic activity for CO2 reduction to formic acid than silicene. Notably, Si‐doped graphene favors formic acid over carbon monoxide, which is similar to silicene. Formic acid to formaldehyde and formaldehyde to methanol conversions have also been studied, sometimes showing improved efficacy of Si‐doped graphene over silicene. The final reduction step, the methanol to methane reaction, occurs in four steps, with the rate‐determining step involving hydrogen transfer from silicon to methyl, whose activation energy is lower than that of silicene. Si‐doped graphene NFs act as better catalysts with lower activation energies than those of silicene. Overall, silicon‐doped graphene enhanced the catalytic activity while maintaining the environmental stability of the graphene. [ABSTRACT FROM AUTHOR]

To protect biodiversity we must understand its structure and composition including the bacteria and microparasites associated with wildlife, which may pose risks to human health. However, acquiring this knowledge often presents challenges, particularly in areas of high biodiversity where there are many undescribed and poorly studied species and funding resources can be limited. A solution to fill this knowledge gap is sampling roadkill (animals that die on roads as a result of collisions with circulating vehicles). These specimens can help characterize local wildlife and their associated parasites with fewer ethical and logistical challenges compared to traditional specimen collection. Here we test this approach by analyzing 817 tissue samples obtained from 590 roadkill vertebrate specimens (Amphibia, Reptilia, Aves and Mammalia) collected in roads within the Tropical Andes of Ecuador. First, we tested if the quantity and quality of recovered DNA varied across roadkill specimens collected at different times since death, exploring if decomposition affected the potential to identify vertebrate species and associated microorganisms. Second, we compared DNA stability across taxa and tissues to identify potential limitations and offer recommendations for future work. Finally, we illustrate how these samples can aid in taxonomic identification and parasite detection. Our study shows that sampling roadkill can help study biodiversity. DNA was recovered and amplified (allowing species identification and parasite detection) from roadkill even 120 hours after death, although risk of degradation increased overtime. DNA was extracted from all vertebrate classes but in smaller quantities and with lower quality from amphibians. We recommend sampling liver if possible as it produced the highest amounts of DNA (muscle produced the lowest). Additional testing of this approach in areas with different environmental and traffic conditions is needed, but our results show that sampling roadkill specimens can help detect and potentially monitor biodiversity and could be a valuable approach to create biobanks and preserve genetic data. [ABSTRACT FROM AUTHOR]

We propose a novel 2D material based on silicon haeckelite (Hck), whose structure contains a silicon atom arranged in a periodic pattern of pentagons and heptagons. Stacking the two layers gives rise to a planar geometry of the layers that compose it. This new structure presents a semiconductor character with a band gap of 0.17 eV. Furthermore, we studied CO2 reduction using molecular hydrogen to form formic acid, carbon monoxide, formaldehyde, methanol, and methane. All these have been studied theoretically at the Grimme D3BJ corrected TPSS/def2-SVP level. A massive biflake containing 132 Si atoms was used to model the Hck surface. According to the results, CO2 capture with Hck is a spontaneous step; in contrast, the same process for silicene mono- and bi-flakes studied previously was endergonic. After the capture of CO2, the addition of H2 to the substrate passes through an intermediate containing a Si–H bond. The formation of Si–H intermediates is the origin of the catalytic effect, facilitating H2 dissociation and acting as the hydrogen atom donor for the substrate. These intermediates are transformed by adding hydrogen atoms and losing water molecules, producing formic acid and formaldehyde as the most probable products, with rate-controlling steps of 29.2 and 27 kcal mol−1, whose values were less than those exhibited by the silicene biflake. This means that the silicon haeckelite biflake presents better catalytic activity than the silicene biflake. The results show that the novel 2D silicon hackelite material has remarkable potential for CO2 capture and reduction. The theoretical analysis of this innovative 2D structure provides valuable insights into the potential applications of silicene-based materials. [ABSTRACT FROM AUTHOR]

The use of renewable energy sources to reduce carbon dioxide (CO2) emissions has gained significant attention in recent years. The catalytic reduction of CO2 into value-added products is a promising approach to achieve this goal, and silicene biflakes (2Si) have been identified as potential candidates for this task. In this study, we explored the catalytic activity of these structures using density functional theory calculations. Our results show that the reaction pathway involves the adsorption of CO2 onto the silicene surface, followed by the addition of hydrogen molecules to form products such as formic acid, methanol, methane, carbon monoxide, and formaldehyde. Our proposed mechanism indicates that silicene biflakes exhibit a higher affinity for CO2 than single-layer silicon. We also found that the hydrogenation with H2 occurs by adding one hydrogen atom to the absorbed CO2 and another to the surface of 2Si. Intermediate species are reduced by systematically adding hydrogen atoms and removing water molecules, forming formic acid as the most probable product. The rate-controlling step for this reaction has an energy of 32.9 kcal mol−1. In contrast, the process without a catalyst shows an energy of 74.6 kcal mol−1, suggesting that the silicon bilayer is a structure with outstanding potential to capture and reduce CO2. Our study provides important insights into the fundamental mechanisms underlying the silicene-mediated CO2 reduction and could facilitate the development of more efficient catalysts for this process. [ABSTRACT FROM AUTHOR]

From density functional theory calculations, we elucidated the reaction mechanism of CO2 reduction on silicene nanoflakes. According to the results, silicene monoflakes present a notable catalytic activity for the hydrogenation of CO2. The most probable energetically favorable reaction pathway is formic acid and formaldehyde production, with energy barriers ranging between 16 and 24.1 kcal/mol. At the same time, transforming carbon dioxide to methanol, carbon monoxide, and methane requires higher activation energies. This theoretical perspective provides significant insights into silicene‐based materials and their potential applications as CO2 conversion to fuel and value‐added chemicals. [ABSTRACT FROM AUTHOR]

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18, 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice Ih). The strongest HBs within H2O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange‐correlation to discriminate among the different examined types of HBs within H2O clusters, (b) the use of the above‐mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri‐ and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H2O clusters. [ABSTRACT FROM AUTHOR]

We used our recently proposed acidity–basicity interplay (ABI) model (Chem. Sci., 2018, 9, 4402) and the Jorgensen secondary interactions hypothesis (JSIH) to rationalise the experimentally observed trends in the formation constants of doubly and triply H-bonded systems with –NH…O=C– and –NH…N– interactions. Unlike the JSIH, the ABI interpretation can explain the trends in the complexation of amide/imide homo- and heterodimers as well as ADA–DAD clusters. We found that the strongest H-bonds play a very important role, a condition which offers an alternative to the well established JSIH to modulate the stability of these relevant systems. [ABSTRACT FROM AUTHOR]

State-of-the-art chemical bonding analyses show that water clusters have a bifunctional catalytic role in the formation of H2SO4 in acid rain. The embedded H2O monomers mitigate the change in the chemical bonding scenario of the rate-limiting step, reducing thereby the corresponding activation energy in accordance with Hammond's postulate. We expect that the insights given herein will prove useful in the elucidation of the catalytic mechanisms of water in inorganic and organic aqueous chemistry. [ABSTRACT FROM AUTHOR]

Thioureas are an important scaffold in organocatalysis because of their ability to form hydrogen bonds that activate substrates and fix them in a defined position, which allows a given reaction to occur. Structures that enhance the acidity of the thiourea are usually used to increase the hydrogen-bonding properties, such as 3,5-bis(trifluoromethyl)phenyl and boronate ureas. Herein, we report the synthesis of bifunctional thioureas with a chiral moiety that include either a trifluoromethyl or methyl group. Their catalytic performance in representative Michael addition reactions was used in an effort to compare the electronic effects of the fluorination at the methyl group. The observed differences concerning yields and ee values cannot be attributed solely to the different steric environments; theoretical results indicate distinct interactions within the corresponding transition states. The calculated transition states show that the fluorinated catalysts have stronger N-H···O and C-H···F hydrogen bonds, while the nonfluorinated systems have C-H···π contacts. These results have shown that a variety of hydrogen-bonding interactions are important in determining the yield and selectivity of thiourea organocatalysis. These details can be further exploited in catalyst design. [ABSTRACT FROM AUTHOR]

Weinvestigate the electronic structure and noncovalent interactionswithin cation–radical complexes that are relevant in the electronimpact mass spectrometry of N-(2-furylmethyl)anilines,4-R–C6H4–NH–CH2–C4H3O with (R = −H, −OCH3, −CH3, −F, −Cl, −Br).In particular, we consider the reactive intermediates that precedethe final products of two previously suggested dissociation pathwaysfor these systems, i.e., (i) a direct cleavage of the NH–CH2bond and (ii) an isomerization/fragmentation mechanism. Thestudy is performed by means of correlated calculations (UCCSD andUMP2) together with density functionals (UM06 an UM06-2x) along withthe triple-ζ quality basis set 6-311++G(2d,2p). In addition,we carried out a topological analysis of the electron density in accordancewith the quantum theory of atoms in molecules (QTAIM) together withthe examination of the noncovalent interaction (NCI) index. In contrastwith previous studies based on the UB3LYP approximation, we coulddetermine the transition states associated with both fragmentationpathways. The Rice–Ramsperger–Kassel–Marcus theory,used to determine the relative importance of these dissociation mechanisms,indicates that whereas the direct cleavage and the isomerization/fragmentationreaction routes have similar constant rates at low energy, the formerprevails when the energy of the system is increased. The QTAIM analysisreveals that the charge of the cation–radical complex is mainlylocated on either a furfuryl (direct cleavage mechanism) or a pyrylium(isomerization/fragmentation pathway) ion and that these units interactwith a neutral radical aniline moiety. The localization of the positivecharge in either a furfuryl or pyrylium cation is in agreement withthe preminecence of the m/z= 81fragment in the mass spectrometry of N-(2-furylmethyl)anilines.Moreover, the QTAIM properties indicate that the α unpairedelectron of the system is principally distributed over the nitrogenand the orthoand paracarbon atomswith respect to the −NH group in the R–C6H4–NH unit. The investigation of the NCI indexand the intermolecular bond critical points and bond paths gives anaccount of the NCIs linking the radical cation clusters under consideration.Finally, we found correlations which indicate that the concentrationof the m/z= 81 fragment in a massspectrum is reduced with the interaction energy of the radical complexfrom which it is originated. Altogether, this work shows how the combinationof suitable electronic structure calculations along with post wavefunction analyses can yield important insights about the formationand properties of cation–radical complexes relevant in massspectrometry. [ABSTRACT FROM AUTHOR]

The energy-dependent branching ratios of the complementaryfragmentions [C5H5O]+and [HC6H4NH]+([M – C5H5O]+), originating from the N-(2-furylmethyl)anilinemolecular ion, [HC6H4NH–C5H5O]+•, were obtained from Rice–Ramsperger–Kassel–Marcus(RRKM) rate calculations based on density functional theory (DFT)energy profiles. The UB3LYP/6-311G+(3df,2p)//UB3LYP/6-31G(d) levelof theory was used to model the competitive reaction mechanisms bywhich the molecular ion can be fragmented. Initially, eight pairsof products were taken into account, corresponding to the combinationof two isomeric structures for each fragment ion and the concomitantradicals, which can be formed by direct dissociations or through someisomerization-fragmentation pathways. A great deal of the obtainedpathways was discarded by looking over the kinetic barrier heightsand the individual RRKM rate coefficients calculated for all the steps.This way, the potential energy profiles were simplified to only threereaction channels, two pathways to [C5H5O]+and one to [M – C5H5O]+. The pre-equilibrium and steady-state approximations were then appliedto different regions of the remaining potential energy profiles, allowingthe branching ratios of the complementary fragment ions to be easilycalculated and discriminated among the three rival processes. Accordingto these results, the major fragment ion in the ion source is [C5H5O]+, which is produced as a mixtureof two structures, the furfuryl and pyrylium cations, one formed bya direct C–N bond cleavage and the other through an isomerization-fragmentationchannel. In turn, the direct fragmentation is the only mechanism toproduce [M – C5H5O]+. To confrontthese results with the available experimental information, the modelwas broadened out to the 4-substituted analogues [4-R–C6H4NH–C5H5O]+•in which R = F, Br, Cl, CH3, and OCH3, findingexcellent correlations of the calculated branching ratios and therelative abundances in the electron ionization mass spectra. [ABSTRACT FROM AUTHOR]

We propose a novel 2D material based on silicon haeckelite (Hck), whose structure contains a silicon atom arranged in a periodic pattern of pentagons and heptagons. Stacking the two layers gives rise to a planar geometry of the layers that compose it. This new structure presents a semiconductor character with a band gap of 0.17 eV. Furthermore, we studied CO 2 reduction using molecular hydrogen to form formic acid, carbon monoxide, formaldehyde, methanol, and methane. All these have been studied theoretically at the Grimme D3BJ corrected TPSS/def2-SVP level. A massive biflake containing 132 Si atoms was used to model the Hck surface. According to the results, CO 2 capture with Hck is a spontaneous step; in contrast, the same process for silicene mono- and bi-flakes studied previously was endergonic. After the capture of CO 2 , the addition of H 2 to the substrate passes through an intermediate containing a Si-H bond. The formation of Si-H intermediates is the origin of the catalytic effect, facilitating H 2 dissociation and acting as the hydrogen atom donor for the substrate. These intermediates are transformed by adding hydrogen atoms and losing water molecules, producing formic acid and formaldehyde as the most probable products, with rate-controlling steps of 29.2 and 27 kcal mol -1 , whose values were less than those exhibited by the silicene biflake. This means that the silicon haeckelite biflake presents better catalytic activity than the silicene biflake. The results show that the novel 2D silicon hackelite material has remarkable potential for CO 2 capture and reduction. The theoretical analysis of this innovative 2D structure provides valuable insights into the potential applications of silicene-based materials.

The use of renewable energy sources to reduce carbon dioxide (CO 2 ) emissions has gained significant attention in recent years. The catalytic reduction of CO 2 into value-added products is a promising approach to achieve this goal, and silicene biflakes (2Si) have been identified as potential candidates for this task. In this study, we explored the catalytic activity of these structures using density functional theory calculations. Our results show that the reaction pathway involves the adsorption of CO 2 onto the silicene surface, followed by the addition of hydrogen molecules to form products such as formic acid, methanol, methane, carbon monoxide, and formaldehyde. Our proposed mechanism indicates that silicene biflakes exhibit a higher affinity for CO 2 than single-layer silicon. We also found that the hydrogenation with H 2 occurs by adding one hydrogen atom to the absorbed CO 2 and another to the surface of 2Si. Intermediate species are reduced by systematically adding hydrogen atoms and removing water molecules, forming formic acid as the most probable product. The rate-controlling step for this reaction has an energy of 32.9 kcal mol -1 . In contrast, the process without a catalyst shows an energy of 74.6 kcal mol -1 , suggesting that the silicon bilayer is a structure with outstanding potential to capture and reduce CO 2 . Our study provides important insights into the fundamental mechanisms underlying the silicene-mediated CO 2 reduction and could facilitate the development of more efficient catalysts for this process.

Complexes of Li, Na, and Mg with graphene, silicene, phosphorene nanoflakes (NFs), and their 2D allotropies have been studied at dispersion corrected TPSS/def-TZVP level of theory. The energy partition analysis of the complexes revealed that for most of the complexes exchange and correlation energies represent dominant contributions to the binding with strong charge transfer from the metal atom to a NF. The exceptions are Mg complexes of graphene and phosphorene NFs where binding is due to dispersion and correlation terms. This difference is also reflected in large Mg-NF distances suggesting weak intermolecular interactions in these complexes. The calculated activation energies for metal hopping are easily achievable at room temperatures for carbon and silicon allotropies. However, they are significantly higher for phosphorus allotropies reaching almost 18 kcal/mol. Generally, activation energies for hopping increase with binding energies for graphene, silicene, and phosphorene NFs. This trend does not observe however for graphene, silicene, and phosphorene 2D allotropies., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The potential energy profiles for the fragmentations that lead to [C(5)H(5)O](+) and [C(4)H(6)](+*) ions from the molecular ions [C(5)H(6)O](+*) of E-2,4-pentadienal were obtained from calculations at the UB3LYP/6-311G + + (3df,3pd)//UB3LYP/6-31G(d,p) level of theory. Kinetic barriers and harmonic frequencies obtained by the density functional method were then employed in Rice-Ramsperger-Kassel-Marcus calculations of individual rate coefficients for a large number of reaction steps. The pre-equilibrium and rate-controlling step approximations were applied to different regions of the complex potential energy surface, allowing the overall rate of decomposition to be calculated and discriminated between three rival pathways: C-H bond cleavage, decarbonylation and cyclization. These processes should have to compete for an equilibrated mixture of four conformers of the E-2,4-pentadienal ions. The direct dissociation, however, can only become important in the high-energy regime. In contrast, loss of CO and cyclization are observable processes in the metastable kinetic window. The former involves a slow 1,2-hydrogen shift from the carbonyl group that is immediately followed by the formation of an ion-neutral complex which, in turn, decomposes rapidly to the s-trans-1,3-butadiene ion [C(4)H(6)](+*). The predominating metastable channel is the second one, that is, a multi-step ring closure which starts with a rate-limiting cis-trans isomerization. This process yields a mixture of interconverting pyran ions that dissociates to the pyrylium ions [C(5)H(5)O](+). These results can be used to rationalize the CID mass spectrum of E-2,4-pentadienal in a low-energy regime., (2010 John Wiley & Sons, Ltd.)

The potential energy profiles for the mutual conversion of the isomeric molecular ions [C5H6O]+* of 2-methylfuran, 3-methylfuran and 4H-pyran and the fragmentations that lead to [C(5)H(5)O](+) ions were obtained from calculations at the B3LYP/6-311G++(3df,3pd)//B3LYP/6-31G(d,p) level of theory. The various competing unimolecular processes were characterized by their RRKM microcanonical rate coefficients, k(E), using the sets of reactant and transition state frequencies and the kinetic barriers obtained from the density functional method. In either a high- or a low-energy regime, the pyrylium ion [C5H5O]+ is generated directly from the 4H-pyran molecular ion by a simple cleavage. In contrast, in the metastable kinetic window, the molecular ions of methylfurans irreversibly isomerize to a mixture of interconverting structures before dissociation, which includes the 2H- and 3H-pyran ions. The hydrogen atoms attached to saturated carbons of the pyran rings are very stabilizing at the position 2, but they are very labile at position 3 and can be shifted to adjacent positions. Once 4H-pyran ion has been formed, the C-H bond cleavage begins before any hydrogen shift occurs. According to our calculation, there would not be complete H scrambling preceding the dissociation of the molecular ions [C5H6O]+*. On the other hand, as the internal energy of the 2-methylfuran molecular ion increases, H* loss can become more important. These results agree with the available experimental data., (Copyright 2009 John Wiley & Sons, Ltd.)