Theoretical Characterization of Germanene Doped with Main Group Elements.

Herein, using density functional calculations, we studied the substitutional doping in germanene with B, C, N, O, Al, Si, P, S, Ga, As, and Se. Nitrogen is the element that can be more easily incorporated into the germanene lattice, followed by silicon, carbon, and boron. Almost all dopants were efficient in opening a band-gap. Yet, caution should be taken because this opening strongly depends on the dopant concentration. Carbon and sulfur were the most effective elements for band-gap opening. C-doping generates the lowest effective masses (me*/m0=mh*/m0=0.09). The equal me and mh values indicate an intrinsic semiconductor behavior, a characteristic shared by the chalcogenides-doped systems. Additionally, we performed a detailed analysis of the preferred disposition of dopants in the germanene lattice. In contrast with the results obtained for graphene, when multiple atoms are introduced in the germanene framework, they do not prefer to be agglomerated, adopting a random disposition, except in the case of sulfur and nitrogen, which favored specific dopant arrangement. Two sulfur dopants showed a notorious preference for replacing a Ge-Ge bond but without forming an S-S linkage, thus adopting a thiophene-like structure that may impart germanene exciting properties, as observed for S and N codoped graphene.

A Theoretical Study on the Mechanisms Involved in Catalytic Dehydrogenation and Dehydration of Isopropanol on SrTiO3.

The dehydrogenation and dehydration of isopropanol on the SrO and TiO2 terminated surfaces, of the SrTiO3 perovskite, is addressed by periodic DFT calculations in order to shed light on the involved mechanisms. The results show that the dehydrogenation occurs through a mechanism involving the dissociative adsorption of the alcohol on the SrO terminated surface, followed the nucleophilic attack of a hydride species on the previously adsorbed hydrogen atom to form molecular hydrogen and the corresponding carbonyl compound. The dehydration instead occurs by the molecular adsorption of the alcohol on the TiO2 terminated surface, followed by various possible E1 elimination pathways leading to the formation of the corresponding alkene and a water molecule. The article reports a thorough study on the involved mechanisms, including identification of the transition states and intermediates along the reaction paths, and evaluation of the respective activation barriers, as well. Thus, this article provides significant insights about the mechanisms of dehydrogenation and dehydration of isopropanol on the SrTiO3 , not reported earlier in literature. The calculated barrier energies are in good agreement with experimental values.

The Solute Polarization and Structural Effects on the Nonlinear Optical Response of Based Chromone Molecules.

The solute polarization due to solvent is a an electrostatic quantum effect that impacts diverse molecular properties, including the nonlinear optical response of a material. An iterative procedure that allows updating the solute charge distribution in the presence of the solvent is combined with a sequential Monte Carlo/Quantum Mechanics methodology and Density Functional Theory methods to evaluate the nonlinear optical (NLO) response using the hyper Rayleigh scattering (HRS) of a series of chromones recently identified in Chamaecrista diphylla, an herbaceous plant abundant throughout the Americas and used in folk medicine. From this study, it is determined that from gas to solvent environment, the systems acquire low refractive index (n) and an improvement of the first hyperpolarizability (ßHRS ), signaling potential NLO uses. It is shown that the octupolar contributions (ßJ=3 ) superate the dipolar ones (ßJ=1 ) and dominate the second-order optical response in both gas and liquid phases, which indicate nontrivial optical materials. Moreover, the solvent environment and structural changes in the periphery can tune significantly the dipolar/octupolar balance, showing a key to control the decoupling between these contributions.

Photodetachment of Deprotonated R-Mandelic Acid: The Role of Proton Delocalization on the Radical Stability.

The photodetachment and stability of R-Mandelate, the deprotonated form of the R-Mandelic acid, was investigated by observing the neutral species issued from either simple photodetachment or dissociative photodetachment in a cold anions set-up. R-Mandalate has the possibility to form an intramolecular ionic hydrogen-bond between adjacent hydroxyl and carboxylate groups. The potential energy surface along the proton transfer (PT) coordinate between both groups (O- …H+ …- OCO) features a single local minima, with the proton localized on the O- group (OH…- OCO). However, the structure with the proton localized on the - OCO group (O- …HOCO) is also observed because it falls within the extremity of the vibrational wavefunction of the OH…- OCO isomer along the PT coordinate. The stability of the corresponding radicals, produced upon photodetachment, is strongly dependent on the position of the proton in the anion: the radicals produced from the OH…- OCO isomer decarboxylate without barrier, while the radicals produced from the O- …HOCO isomer are stable.

Infrared Spectroscopy Evidence of Weak Interactions in Frustrated Lewis Pairs Formed by Tris(pentafluorophenyl)borane.

Frustrated Lewis pairs (FLPs) have been widely investigated as promising catalysts due to their metal-free feature and ability to activate small molecules. Since their discovery, many works have been investigating how these Lewis pairs (intermolecular pairs) are held together in an encounter complex. This prompted several studies based on theoretical investigations, but experimental ones are limited yet. In this communication we show evidence of weak intermolecular interactions between Lewis acids and Lewis bases, distinguishing the Lewis adduct from FLPs, by probing fluorine-carbon vibrational modes using infrared spectroscopy. The main evidence is based on the band shifts occurring in FLPs due to weak hydrogen bonds between the hydrogen atoms of the Lewis base and the fluorine atoms of Lewis acid.

Ethanol Oxidation Reaction Mechanism on Gold Nanowires from Density Functional Theory.

Thin gold nanowires (NWs) are materials that could be used as support in different chemical reactions. Using density functional theory (DFT) it was shown that NWs that form linear atomic chains (LACs) are suitable for stimulating chemical reactions. To this end, the oxidation reaction of ethanol supported on the LACs of Au-NWs was investigated. Two types of LACs were used for the study, one pure and the other with an oxygen impurity. The results showed that the oxygen atom in the LAC fulfills important functions throughout the reaction pathway. Before the chemical reaction, it was observed that the LAC with impurity gains structural stability, that is, the oxygen acts as an anchor for the gold atoms in the LAC. In addition, the LAC was shown to be sensitive to disturbances in its vicinity, which modifies its nucleophilic character. During the chemical reaction, the oxidation of ethanol occurs through two different reaction paths and in two stages, both producing acetaldehyde (CH3 CHO). The different reaction pathways are a consequence of the presence of oxygen in the LAC (oxygen conditions the formation of reaction intermediates). In addition, the oxygen in the LAC also modifies the kinetic behavior in both reaction stages. It was observed that, by introducing an oxygen impurity in the LAC, the activation energy barriers decrease ∼69 % and ∼97 % in the first and second reaction stages, respectively.

Influence of LiTaO3 (0001) and KTaO3 (001) Perovskites Structures on the Molecular Adsorption of Styrene and Styrene oxide: A Theoretical Insight by Periodic DFT Calculations.

In this research, the adsorption of styrene and styrene oxide, both biomass derivatives, on KTaO3 (001) and LiTaO3 (0001) perovskite-like structures was studied from a theoretical point of view. The study was carried out using density functional theory (DFT) calculations. The adsorption phenomenon was deeply studied by calculating the adsorption energies (Eads ), adsorbate-surface distances (Å) and evaluating the differences of charge density and charge transfer (ΔCT). For complexes adsorbed on KTaO3 (TaO2 , KO and K(OH)2 exposed layers), the highest Eads was found for styrene oxide, attributed to the oxygen reactivity of the epoxy group describing a strong interaction with the surface. However, when evaluating a K(O)2 model, a more favorable interaction of styrene with the surface is observed, resulting in a high Eads of -9.9 eV and a ΔCT of 3.1e. For LiTaO3 , more favorable interactions are found for both adsorbates compared to KTaO3 , evidenced by the higher adsorption energies and charge density differences, particularly for the styrene complex adsorbed on TaO2 exposed layer (Eads : -10.2 eV). For the LiO termination, the surface exposed oxygens are fundamental for the adsorption of styrene and styrene oxide, leading to a considerable structural distortion. The obtained results thus provide understanding of the structural features, surface reactivity and adsorption sites of LiTaO3 and KTaO3 perovskite in the context of a heterogeneous catalytic process, such as the oxidation of styrene.

Bowl-shaped Cluster CuB12 - : A Viable Global Minimum with Twofold Aromaticity.

A low-lying structure is revealed for the CuB12 - cluster, which is bowl-shaped. It consists of a triangular CuB2 base and a B10 rim. Molecular dynamics simulations indicates its structural robustness; at an elevated temperature (600 K), the base rotates reversibly within the B10 perimeter. Chemical bonding analysis detects 2σ- and 3π-delocalized bonds, suggesting double aromaticity. This is also confirmed by two diatropic and concentric ring currents under an external magnetic field.

Theoretical Study on the Selective 1,2-Reduction of α,ß-Unsaturated Ketones by Hydrogen Transfer Reaction on MgO(100).

Catalytic reduction of α,ß-unsaturated ketones with MgO has been found to improve selectivity to the desired unsaturated alcohol product. Using density functional calculations, we have studied the competitive hydrogenation of C=O and C=C bonds on Mg(100) employing two α,ß-unsaturated ketones: mesityl oxide (MO) and 2-cyclohexenone (CH), with isopropanol (IPA) as hydrogen source. For both ketones, MgO promotes the formation of a six-membered cyclic transition state for selective C=O reductions via a Meerwein-Ponndorf-Verley mechanism. Similar concerted mechanism is also possible for the C=C hydrogenation following an Eley-Rideal mechanism, in which the IPA interacts directly with the adsorbed ketone. The activation barriers are smaller for C=O reduction because this bond is activated on MgO(100). The selective C=O reduction is more favorable for CH than for MO due to the tendency of CH to be perpendicularly oriented. The desorption energies of the unsaturated alcohol are lower than the subsequent C=C reductions.

Understanding the Deactivating/Activating Mechanisms in Three Optical Chemosensors Based on Crown Ether with Na+ /K+ Selectivity Using Quantum Chemical Tools.

The optical properties and transduction mechanisms in three reported optical chemosensors based on crown ether with selectivity turn-on luminescence toward Na+ over K+ , were investigated using Density Functional Theory/Time-Dependent Density Functional Theory (DFT/TD-DFT). The analysis of the structural stability of the conformers enables us to understand the optical properties of the sensors and their selectivity toward Na+ . The UV-Vis absorption and the radiative channels of the adiabatic S1 excited state were assessed. In these reported sensors, the Photoinduced Electron Transfer (PET) from the nitrogen and the oxygen (O-atoms of the substituted N-phenylaza group) lone pairs to fluorophore groups lead to a nonradiative deactivation process in the fluorophore to p-conjugated anilino-1,2,3-triazol ionophore. This Intramolecular Charge Transfer (ICT) deactivation produced the luminescence quenching in the free sensors and K+ /C1 complexes. The Na+ /sensor interaction produced a Chelation Enhanced Fluorescence (CHEF) due to the inhibition of the PET and ICT, which was confirmed via the calculated oscillator strength of the emission process. The K+ /sensor interaction displayed the possibility of PET in C3; however, this fact was inconclusive to affirm the quenching of luminescence, the CHEF in C2 and C3 and the selectivity toward Na+ over K+ in these systems. For this reason, simulation of the absorption and emissions spectra (calculated oscillator strength), calculation of the kinetic parameters (in charge transfers and radiative deactivations process), analysis of the metal-ligand interaction character, and the analysis of the structural stability of the conformers were determinant factors to understand the selectivity and the optical properties of these chemosensors. The results suggest that these theoretical tools can also be used to predict the optical properties and Na+ /K+ selectivity of optical chemosensors.

Jahn-Teller Effects in a Vanadate-Stabilized Manganese-Oxo Cubane Water Oxidation Catalyst.

Heuristic rules that allow identifying the preferred mixed-valence isomers and Jahn-Teller axis arrangements in the water oxidation catalyst [(Mn4 O4 )(V4 O13 )(OAc)3 ]n- and its activated form [(Mn4 O4 )(V4 O13 )(OAc)2 (H2 O)(OH)]n- are derived. These rules are based on computing all combinatorially possible mixed-valence isomers and Jahn-Teller axis arrangements of the MnIII atoms, and associate energetic costs with some structural features, like crossings of multiple Jahn-Teller axes, the location of these axes, or the involved ligands. It is found that the different oxidation states localize on different Mn centers, giving rise to clear Jahn-Teller distortions, unlike in previous crystallographic findings where an apparent valence delocalization was found. The low barriers that connect different Jahn-Teller axis arrangements suggest that the system quickly interconverts between them, leading to the observation of averaged bond lengths in the crystal structure. We conclude that the combination of cubane-vanadate bonds that are chemically inert, cubane-acetate/water bonds that can be activated through a Jahn-Teller axis, and low activation barriers for intramolecular rearrangement of the Jahn-Teller axes plays an essential role in the reactivity of this and probably related compounds.

Spectral Signatures of Oxidation States in a Manganese-Oxo Cubane Water Oxidation Catalyst.

We report IR and UV/Vis spectroscopic signatures that allow discriminating between the oxidation states of the manganese-based water oxidation catalyst [(Mn4 O4 )(V4 O13 )(OAc)3 ]3- . Simulated IR spectra show that V=O stretching vibrations in the 900-1000 cm-1 region shift consistently by about 20 cm-1 per oxidation equivalent. Multiple bands in the 1450-1550 cm-1 region also change systematically upon oxidation/reduction. The computed UV/Vis spectra predict that the spectral range above 350 nm is characteristic of the managanese-oxo cubane oxidation state, whereas transitions at higher energy are due to the vanadate ligand. The presence of absorption signals above 680 nm is indicative of the presence of MnIII atoms. Spectroelectrochemical measurements of the oxidation from [Mn 2 III Mn 2 IV ] to [Mn 4 IV ] showed that the change in oxidation state can indeed be tracked by both IR and UV/Vis spectroscopy.

Role of the solvent in the activation of Li2S as cathode material: a DFT study.

Lithium-sulfur batteries are considered one of the possible next-generation energy-storage solutions, but to be commercially available many drawbacks have yet to be solved. One solution with great potentiality is the use of lithium sulfide as cathode material since it can be coupled to Li-free anodes, such as graphite, Si or Sn. Nevertheless, Li2S, like sulfur, is electronically and ionically insulating, with a high activation potential for its initial oxidation step. To overcome this issue, different strategies have been explored, one of them being the use of catalytic surfaces. In the present article, we study using first principles calculations the effect of the dielectric constant of the solvent on the activation energy of the cleavage reaction of Li2S on different catalytic surfaces. To the best of our knowledge, this is the first time that such a study is undertaken. We find that the effect of the solvent should be twofold: on one side, it should decrease the interaction between the Li2S molecule and the surface. On the other side, since the species arising in the dissociation reaction are charged, the solvent should decrease the activation barrier for the dissociation of the Li2S molecule, when compared with the reaction in vacuum. These theoretical findings are discussed in connection with experimental results from the literature, where the behaviour of the Li-S cathode is studied in different solvents.

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 computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack.

In the present work, the fast amide bond cleavage of [3-((1R,5S,7s)-3-azabicyclo[3.3.1]nonane-7-carbonyl)-3-azabicyclo[3.3.1]nonane-7-carboxylic acid (bi-ATDO)], through an intramolecular nucleophilic attack of an amine group is evaluated. First, six possible peptide bond cleavage mechanisms, two of them including a water molecule, are described at the ωB97XD/6-311 + G(d,p)//MP2/6-311 + G(d,p) level of theory. The reaction consisting of an intramolecular nitrogen nucleophilic attack followed by a proton transfer and the amide bond cleavage is determined as the most favorable mechanism. The activation free energy computed for the latter is 20.5 kcal mol-1 , which agrees with the reported experimental result of 24.8 kcal mol-1 . Inclusion of a water molecule to assist the first step of the reaction results in an activation free energy increase of about 17 kcal mol-1 . All the steps in the most favorable mechanism are studied more in detail employing intrinsic reaction coordinate as well as the reaction force and reaction electronic flux analysis.

Understanding the Chloride Affinity of Barbiturates for Anion Receptor Design.

Due to their potential binding sites, barbituric acid (BA) and its derivatives have been used in metal coordination chemistry. Yet their abilities to recognize anions remain unexplored. In this work, we were able to identify four structural features of barbiturates that are responsible for a certain anion affinity. The set of coordination interactions can be finely tuned with covalent decorations at the methylene group. DFT-D computations at the BLYP-D3(BJ)/aug-cc-pVDZ level of theory show that the C-H bond is as effective as the N-H bond to coordinate chloride. An analysis of the electron charge density at the C-H⋅⋅⋅Cl- and N-H⋅⋅⋅Cl- bond critical points elucidates their similarities in covalent character. Our results reveal that the special acidity of the C-H bond shows up when the methylene group moves out of the ring plane and it is mainly governed by the orbital interaction energy. The amide and carboxyl groups are the best choices to coordinate the ion when they act together with the C-H bond. We finally show how can we use this information to rationally improve the recognition capability of a small cage-like complex that is able to coordinate NaCl.

Computational and Experimental Study of Turbo-Organomagnesium Amide Reagents: Cubane Aggregates as Reactive Intermediates in Pummerer Coupling.

The dynamic equilibria of organomagnesium reagents are known to be very complex, and the relative reactivity of their components is poorly understood. Herein, a combination of DFT calculations and kinetic experiments is employed to investigate the detailed reaction mechanism of the Pummerer coupling between sulfoxides and turbo-organomagnesium amides. Among the various aggregates studied, unprecedented heterometallic open cubane structures are demonstrated to yield favorable barriers through a concerted anion-anion coupling/ S-O cleavage step. Beyond a structural curiosity, these results introduce open cubane organometallics as key reactive intermediates in turbo-organomagnesium amide mixtures.

Dual Emission of meso-Phenyleneethynylene-BODIPY Oligomers: Synthesis, Photophysics, and Theoretical Optoelectronic Study.

Two series of 2,5-di(butoxy)phenyleneethynylenes, one halogenated (nPEC4-X; n=2, 3, or 4) and the other boron-dipyrromethene (BODIPY) terminated (nPEC4-By; n=3, 4, or 5; By=BODIPY), were synthesized monodirectionally by the step-by-step approach and the molecular structure was corroborated by NMR spectroscopy (1 H, 13 C-DEPTQ-135, COSY, HSQC, HMBC, 11 B, 19 F) and MALDI-TOF mass spectrometry. The multiplicity and J-coupling constants of 1 H, 11 B, and 19 F/11 B NMR signals revealed, in the nPEC4-By series, that the phenyl in the meso position of BODIPY becomes electronically part of the conjugation of the phenyleneethynylene chain, whereas BODIPY is electronically isolated. The photophysical, electrochemical, and theoretical studies confirm this finding because the properties of nPEC4-By are comparable to those of the nPEC4-X oligomers and BODIPY, indicating negligible electron communication between BODIPY and the nPEC4 moieties. Nevertheless, energy transfer (ET) from nPEC4 to BODIPY was rationalized by spectroscopy and theoretical calculations. Its yield decreases with the nPEC4 conjugation length, according to the increase in distance between the two chromophores, resulting in dual emission for the longest oligomer in which ET is quenched.

On the Interaction between Deprotonated Cytosine [C(-H) ]- and Ba2+ : Infrared Multiphoton Spectroscopy and Dynamics.

Gas-phase interactions between Ba2+ and deprotonated cytosine (C(-H) ) were studied in [C(-H) Ba]+ and [C(-H) BaC]+ complexes by IRMPD spectroscopy coupled to tandem mass-spectrometry in combination with DFT calculations. For the [C(-H) BaC]+ complex only one [C(-H) KAN1O-Ba-Canti ]+ isomer was found, although the presence of another structure cannot be excluded. This isomer features a central tetracoordinated Ba2+ that simultaneously interacts with keto-amino [C(-H) ]- deprotonated on N1 and neutral keto-amino C. Both moieties are in different planes as a consequence of an additional NH…O=C hydrogen bond between C and [C(-H) ]- . A sequential IRMPD dynamics is observed in this complex. For the [C(-H) Ba]+ complex produced by electrospray ionization two isomers ([C(-H) KAN1OBa]+ and [C(-H) KAN3OBa]+ ) were identified, in which Ba2+ interacts simultaneously with the C=O group and the N1 or N3 atom of the keto-amino [C(-H) ]- , respectively. A comparison with the related [C(-H) Pb]+ complex (J. Y. Salpin et al., Chem. Phys. Chem. 2014, 15, 2959-2971) is also presented.

Substituent Effects on NMR Spectroscopy of 2,2-Dimethylchroman-4-one Derivatives: Experimental and Theoretical Studies.

The attribution of 1H and 13C NMR signals of a library of 5-, 6- and 7-substituted 2,2-dimethylchroman-4-one derivatives is reported. Substituent effects were interpreted in terms of the Hammett equation, showing a good correlation for carbons para- to the substituent group, not for the meta- ones. Similarly, the Lynch correlation shows the additivity of the substituent chemical shifts in the case of both H and C nuclei, again with the exception of the carbons in the meta- position. Density Functional Theory (DFT)-predicted 1H and 13C chemical shifts correspond closely with experimentally observed values, with some exceptions for C NMR data; however, the correlation is valid only for the aromatic moiety and cannot be extended to the heterocyclic ring of the chroman-4-one scaffold.