(Ro)vibrational Spectroscopic Constants, Lifetime and QTAIM Evaluation of Fullerene Dimers Stability.

The iconic caged shape of fullerenes gives rise to a series of unique chemical and physical properties; hence a deeper understanding of the attractive and repulsive forces between two buckyballs can bring detrimental information about the structural stability of such complexes, providing significant data applicable for several studies. The potential energy curves for the interaction of multiple van der Waals buckyball complexes with increasing mass were theoretically obtained within the DFT framework at ωB97xD/6-31G(d) compound model. These potential energy curves were employed to estimate the spectroscopic constants and the lifetime of the fullerene complexes with the Discrete Variable Representation and with the Dunham approaches. It was revealed that both methods are compatible in determining the rovibrational structure of the dimers and that they are genuinely stable, i.e., long-lived complexes. To further inquire into the nature of such interaction, Bader's QTAIM approach was applied. QTAIM descriptors indicate that the interactions of these closed-shell systems are dominated by weak van der Waals forces. This non-covalent interaction character was confirmed by the RDG analysis scheme. Indirectly, QTAIM also allowed us to confirm the stability of the non-covalent bonded fullerene dimers. Our lifetime calculations have shown that the studied dimers are stable for more than 1 ps, which increases accordingly with the number of carbon atoms.

Theoretical study of the interaction of fullerenes with the emerging contaminant carbamazepine for detection in aqueous environments.

The global increase in drug consumption exposes the growing need to develop new systems for the detection, capture, and treatment of bioactive molecules. Carbamazepine is one instance of such contaminants at the top of the ranking commonly found in sewage treatment systems. This work, therefore, presents a theoretical study of fullerene C60 and its derivatives with substitutional doping with B, Al, Ga, Si, Ge, N and P, for the detection and capture of carbamazepine is aqueous medium. Solvation effects were included by means of the Polarizable Continuum Solvent method. The results indicate that doped fullerenes are sensitive for the detection of carbamazepine both in gaseous and aquatic environments. Investigation on the intermolecular interactions between the drug and the fullerene molecule were carried out, allowing the characterization of the interactions responsible for stabilizing the adsorption of carbamazepine to the fullerenes. The theoretical survey revealed that fullerenes doped with Al, Ga, Si and Ge chemically adsorb carbamazepine whereas for the case of fullerenes doped with other heteroatoms physisorption is responsible for the molecular recognition. Relying on DFT calculations, the fullerene derivatives C59Al, C59Si and C59Ga are the most suitable to act both as a sensor and to uptake carbamazepine in aquatic environments.

Harnessing Greenhouse Gases Absorption by Doped Fullerenes with Externally Oriented Electric Field.

In this work, a theoretical investigation of the effects caused by the doping of C20 with silicon (Si) atom as well as the adsorption of CO, CO2 and N2 gases to C20 and C19Si fullerenes was carried out. In concordance with previous studies, it was found that the choice of the doping site can control the structural, electronic, and energetic characteristics of the C19Si system. The ability of C20 and C19Si to adsorb CO, CO2 and N2 gas molecules was evaluated. In order to modulate the process of adsorption of these chemical species to C19Si, an externally oriented electric field was included in the theoretical calculations. It was observed that C19Si is highly selective with respect to CO adsorption. Upon the increase of the electric field intensity the adsorption energy was magnified correspondingly and that the interaction between CO and C19Si changes in nature from a physical adsorption to a partial covalent character interaction.

Fluorescent Benzoselenadiazoles: Synthesis, Characterization, and Quantification of Intracellular Lipid Droplets and Multicellular Model Staining.

In this work, we described the synthesis of 10 new fluorescent 2,1,3-benzoselenadiazole small-molecule derivatives and their chemical- and photocharacterizations. The new derivatives could, for the first time, be successfully applied as selective live cell imaging probes (at nanomolar concentrations) and stained lipid-based structures preferentially. Density functional theory (DFT) calculations were used to help in understanding the photophysical data and the intramolecular charge-transfer (ICT) processes of the synthesized dyes. Some derivatives showed impressive cellular responses, allowing them to be tested as probes in a complex multicellular model (i.e., Caenorhabditis elegans). When compared with the commercially available dye, the new fluorescent compounds showed far better results both at the cellular level and inside the live worm. Inside the multicellular complex model, the tested probes also showed selectivity, a feature not observed when the commercial dye was used to carry out the bioimaging experiments.

Kinetics of the OH+HCl→H2 O+Cl reaction: Rate determining roles of stereodynamics and roaming and of quantum tunneling.

The OH + HCl → H2 O + Cl reaction is one of the most studied four-body systems, extensively investigated by both experimental and theoretical approaches. Here, as a continuation of our previous work on the OH + HBr and OH + HI reactions, which manifest an anti-Arrhenius behavior that was explained by stereodynamic and roaming effects, we extend the strategy to understand the transition to the sub-Arrhenius behavior occurring for the HCl case. As previously, we perform first-principles on-the-fly Born-Oppenheimer molecular dynamics calculations, thermalized at four temperatures (50, 200, 350, and 500 K), but this time we also apply a high-level transition-state-theory, modified to account for tunneling conditions. We find that the theoretical rate constants calculated with Bell tunneling corrections are in good agreement with extensive experimental data available for this reaction in the ample temperature range: (i) simulations show that the roles of molecular orientation in promoting this reaction and of roaming in finding the favorable path are minor than in the HBr and HI cases, and (ii) dominating is the effect of quantum mechanical penetration through the energy barrier along the reaction path on the potential energy surface. The discussion of these results provides clarification of the origin on different non-Arrhenius mechanisms observed along this series of reactions. © 2018 Wiley Periodicals, Inc.

The influence of the configuration of the (C70)2 dimer on its rovibrational spectroscopic properties: a theoretical survey.

A study of the spectroscopic properties of the buckyball dimer (C70)2 was performed, which involved mapping the potential energy curve of this system. The spectroscopic constants of the system were obtained using theoretical Dunham and discrete variable representation methods, as well as the Rydberg analytical function expanded to the sixth degree. Because the fullerenes in the dimer have both hexagonal and pentagonal faces, the properties of (C70)2 were examined for different system configurations. The fullerene dimerization process involves a weak interaction, possibly mediated by short-range components such as van der Waals forces. The differences between the spectroscopic constants of the various (C70)2 configurations and between their dissociation energies De were found to be rather small, which can be attributed to the dominant influence of the hexagonal faces of the fullerenes on the interaction between the fullerenes. These results should aid our understanding of the process of fullerene dimer formation and hopefully facilitate the development and application of new materials based on these dimers. Graphical Abstract Comparison of the potential energy curve and a schematic representation for the all (C70)2 fullerenes dimers configurations.

Explicit Aqueous Solvation Treatment of Epinephrine from Car-Parrinello Molecular Dynamics: Effect of Hydrogen Bonding on the Electronic Absorption Spectrum.

The electronic absorption spectrum of the neurotransmitter epinephrine (EPN) in water solution is studied, combining ab initio Car-Parrinello molecular dynamics (CPMD) with a quantum mechanical approach within the framework of the time-dependent density functional theory (TDDFT) scheme. By selecting 52 uncorrelated snapshots, the excitation modes were calculated at the LC-ωPBE/6-31+G(d) level of theory, using an optimal range-separation parameter ω, determined by means of the gap-tuning scheme in the presence of the solvent molecules. By comparing with static approaches (vacuum and implicit solvation), we show here that explicit solvation treatment dramatically enhances the photophysical properties of the EPN, especially because of the more realistic dynamic description of the molecular geometry. The agreement between the simulated and experimental spectra is demonstrated when TDDFT calculations are performed with the optimally tuned version of the DFT hybrid, not only improving the relative intensities of the absorption bands but also the λmax position. These results highlight that accounting for the nuclear motions, that is, thermal effects (of both chromophore and solvent molecules), is imperative to predict experimental absorption spectra. In this paper, we have addressed the critical importance of explicit solvation effects on the photophysics of the EPN, raking in performance when the simulation is performed based on first-principles molecular dynamics such as CPMD.

From Live Cells to Caenorhabditis elegans: Selective Staining and Quantification of Lipid Structures Using a Fluorescent Hybrid Benzothiadiazole Derivative.

The current article describes the synthesis, characterization, and application of a designed hybrid fluorescent BTD-coumarin (2,1,3-benzothiadiazole-coumarin) derivative (named BTD-Lip). The use of BTD-Lip for live-cells staining showed excellent results, and lipid droplets (LDs) could be selectively stained. When compared with the commercially available dye (BODIPY) for LD staining, it was noted that the designed hybrid fluorescence was capable of staining a considerable larger number of LDs in both live and fixed cells (ca. 40% more). The new dye was also tested on live Caenorhabditis elegans (complex model) and showed an impressive selectivity inside the worm, whereas the commercial dye showed no selectivity in the complex model.

Bond Ellipticity Alternation: An Accurate Descriptor of the Nonlinear Optical Properties of π-Conjugated Chromophores.

Well-defined structure-property relationships offer a conceptual basis to afford a priori design principles to develop novel π-conjugated molecular and polymer materials for nonlinear optical (NLO) applications. Here, we introduce the bond ellipticity alternation (BEA) as a robust parameter to assess the NLO characteristics of organic chromophores and illustrate its effectiveness in the case of streptocyanines. BEA is based on the symmetry of the electron density, a physical observable that can be determined from experimental X-ray electron densities or from quantum-chemical calculations. Through comparisons to the well-established bond-length alternation and π-bond order alternation parameters, we demonstrate the generality of BEA to foreshadow NLO characteristics and underline that, in the case of large electric fields, BEA is a more reliable descriptor. Hence, this study introduces BEA as a prominent descriptor of organic chromophores of interest for NLO applications.

A novel analytical potential function for dicationic diatomic molecular systems based on deformed exponential function.

In this paper, we propose a new alternative analytical function aiming to better describe the potential energy curves of the doubly charged diatomic molecules. To achieve this goal, we modified an existing potential function in the literature to describe dicationic diatomic molecules using the deformed exponential function. We generated the potential energy curve of the testing group of dicationic diatomic molecules [Formula: see text], BH2+, [Formula: see text] and NH2+ by means of the CCSD(T)/aug-cc-pVQZ level of theory. To validate this new function, we also calculated the spectroscopic constants and the rovibrational spectra for the electronic state [Formula: see text]of the [Formula: see text] and [Formula: see text] systems using the Dunham and discrete variable representation methods. For BH2+ and NH2+ molecules, despite exhibiting a local minimum in the potential energy curve, no vibrational levels are supported, so the spectroscopic constants for these poorly bound systems are invalidated. The fitting accuracy had a better performance over the original potential for describing dicationic diatomic systems, considering that the discrete variable representation method resulted in a similar vibrational structure described in the literature. This fact can be explained due to the deformed function's flexibility.

Charge-tagged N-heterocyclic carbenes (NHC): Direct transfer from ionic liquid solutions and long-lived nature in the gas phase.

Negatively charge-tagged N-heterocyclic carbenes have been formed in solution via deprotonation of imidazolium ions bearing acid side groups and transferred to the gas phase via ESI(-)-MS. The structure of the putative and apparently stable gaseous carbenes formed in such conditions were then probed via reactions with carbon dioxide using a triple quadrupole mass spectrometer particularly optimized for ion/molecule reactions of ESI-generated ions. Complete conversion to imidazolium carboxylates was achieved, which seems to demonstrate the efficiency of the transfer, the gas-phase stability, and the long-lived nature of these unprecedented charge-tagged carbenes and their predominance in the ionic population. Comprehensive studies on the intrinsic reactivity of N-heterocyclic carbenes with silent charge tags are therefore possible. Graphical Abstract ᅟ.

Effect of the crystalline environment on the third-order nonlinear optical properties of L-arginine phosphate monohydrate: a theoretical study.

A supermolecular approach combined with an iterative electrostatic scheme was employed to investigate the nonlinear optical properties of the hybrid L-arginine phosphate monohydrate crystal, the procedure being aided by DFT calculations. The supermolecular scheme basically treated the molecules surrounding the unit cell as point charges; this approximation results in rapid convergence, making it a feasible method. DFT functionals of different flavors were considered: B3LYP, B2PLYP, CAM-B3LYP, ωB97, and M06HF, utilizing the 6-311 + G(d) basis set. All functionals gave sufficiently accurate values for the dipole moment (µ) with respect to the experimental value 32(2) D. For the average linear polarizability ([Formula: see text]) and the total first hyperpolarizability (ß tot), good agreement was observed between the DFT-calculated values and MP2-derived results reported in the literature. For the second hyperpolarizability, both static and dynamic regimes were considered. The point-charge embedding approach led to an attenuation of the second hyperpolarizability γ for all frequencies considered. Excitations of γ were not observed for frequencies smaller than 0.1 a.u. For the second hyperpolarizability (both static and dynamic), computational results showed that L-arginine phosphate monohydrate exhibits a large nonlinear optical effect, which implies the occurrence of microscopic third-order NLO behavior.

Deformed transition-state theory: Deviation from Arrhenius behavior and application to bimolecular hydrogen transfer reaction rates in the tunneling regime.

A formulation is presented for the application of tools from quantum chemistry and transition-state theory to phenomenologically cover cases where reaction rates deviate from Arrhenius law at low temperatures. A parameter d is introduced to describe the deviation for the systems from reaching the thermodynamic limit and is identified as the linearizing coefficient in the dependence of the inverse activation energy with inverse temperature. Its physical meaning is given and when deviation can be ascribed to quantum mechanical tunneling its value is calculated explicitly. Here, a new derivation is given of the previously established relationship of the parameter d with features of the barrier in the potential energy surface. The proposed variant of transition state theory permits comparison with experiments and tests against alternative formulations. Prescriptions are provided and implemented to three hydrogen transfer reactions: CH4 + OH → CH3 + H2 O, CH3 Cl + OH → CH2 Cl + H2 O and H2 + CN → H + HCN, widely investigated both experimentally and theoretically. © 2016 Wiley Periodicals, Inc.

Stereodirectional Origin of anti-Arrhenius Kinetics for a Tetraatomic Hydrogen Exchange Reaction: Born-Oppenheimer Molecular Dynamics for OH + HBr.

Among four-atom processes, the reaction OH + HBr → H2O + Br is one of the most studied experimentally: its kinetics has manifested an unusual anti-Arrhenius behavior, namely, a marked decrease of the rate constant as the temperature increases, which has intrigued theoreticians for a long time. Recently, salient features of the potential energy surface have been characterized and most kinetic aspects can be considered as satisfactorily reproduced by classical trajectory simulations. Motivation of the work reported in this paper is the investigation of the stereodirectional dynamics of this reaction as the prominent reason for the peculiar kinetics: we started in a previous Letter ( J. Phys. Chem. Lett. 2015 , 6 , 1553 - 1558 ) a first-principles Born-Oppenheimer "canonical" molecular dynamics approach. Trajectories are step-by-step generated on a potential energy surface quantum mechanically calculated on-the-fly and are thermostatically equilibrated to correspond to a specific temperature. Here, refinements of the method permitted a major increase of the number of trajectories and the consideration of four temperatures -50, +200, +350, and +500 K, for which the sampling of initial conditions allowed us to characterize the stereodynamical effect. The role is documented of the adjustment of the reactants' mutual orientation to encounter the entrance into the "cone of acceptance" for reactivity. The aperture angle of this cone is dictated by a range of directions of approach compatible with the formation of the specific HOH angle of the product water molecule; and consistently the adjustment is progressively less effective the higher the kinetic energy. Qualitatively, this emerging picture corroborates experiments on this reaction, involving collisions of aligned and oriented molecular beams, and covering a range of energies higher than the thermal ones. The extraction of thermal rate constants from this molecular dynamics approach is discussed and the systematic sampling of the canonical ensemble is indicated as needed for quantitative comparison with the kinetic experiments.

Synthesis, Structure, Properties, and Bioimaging of a Fluorescent Nitrogen-Linked Bisbenzothiadiazole.

This paper describes the synthesis, structure, photophysical properties, and bioimaging application of a novel 2,1,3-benzothiadiazole (BTD)-based rationally designed fluorophore. The capability of undergoing efficient stabilizing processes from the excited state allowed the novel BTD derivative to be used as a stable probe for bioimaging applications. No notable photobleaching effect or degradation could be observed during the experimental time period. Before the synthesis, the molecular architecture of the novel BTD derivative was evaluated by means of DFT calculations to validate the chosen design. Single-crystal X-ray analysis revealed the nearly flat characteristics of the structure in a syn conformation. The fluorophore was successfully tested as a live-cell-imaging probe and efficiently stained MCF-7 breast cancer cell lineages.

Stereodynamical Origin of Anti-Arrhenius Kinetics: Negative Activation Energy and Roaming for a Four-Atom Reaction.

The OH + HBr → H2O + Br reaction, prototypical of halogen-atom liberating processes relevant to mechanisms for atmospheric ozone destruction, attracted frequent attention of experimental chemical kinetics: the nature of the unusual reactivity drop from low to high temperatures eluded a variety of theoretical efforts, ranking this one among the most studied four-atom reactions. Here, inspired by oriented molecular-beams experiments, we develop a first-principles stereodynamical approach. Thermalized sets of trajectories, evolving on a multidimensional potential energy surface quantum mechanically generated on-the-fly, provide a map of most visited regions at each temperature. Visualizations of rearrangements of bonds along trajectories and of the role of specific angles of reactants' mutual approach elucidate the mechanistic change from the low kinetic energy regime (where incident reactants reorient to find the propitious alignment leading to reaction) to high temperature (where speed hinders adjustment of directionality and roaming delays reactivity).

Effect of the methanol molecule on the stabilization of C18H18O4 crystal: combined theoretical and structural investigation.

The ability of the chalcone, C18H18O4, to form solvates was theoretically and experimentally investigated. The unit cell with Z' > 1, composed of two independent chalcone molecules (α and ß), shows the formation of a stable molecular complex which is related with the presence of methanol in this crystal lattice. Aiming to understand the process of crystal lattice stabilization, a combination of techniques was used, including X-ray diffraction (XRD), computational molecular modeling, and an ab initio molecular dynamic. The results show that α and ß molecules are sterically barred from forming a direct hydrogen bond with one other. In addition, the presence of the methanol molecule stabilizes the crystal structure by a bifurcated O-H···O interaction acting as a bridge between them. The theoretical thermodynamic parameter and the rigid potential energy surface scan describe the role of methanol in the energy stabilization of the crystal. The absence of the methanol compound in the asymmetric unit destabilizes the crystalline structure, making the formation process of the asymmetric unit nonspontaneous. The energy difference between α and ß molecules is around 0.80 kcal·mol(-1), indicating that both are stable and equally possible in the crystal lattice. The analysis of the energy profile of the C14-O2···H1-O3 and O2-H1···O3-C17 torsion angles in the crystal packing shows that the α and ß molecules are confined in the stable potential region, in agreement with the two conformers in the asymmetric unit. The Molecular Electrostatic Potential (MEP) shows that the methanol has no steric effects, which prevents small motion around the torsion angles.

Designed benzothiadiazole fluorophores for selective mitochondrial imaging and dynamics.

A series of new rationale designed 2,1,3-benzothiadiazole (BTD) fluorescent derivatives has been synthesized and applied for cellular selective staining of cancer cells in cell-imaging experiments. Four new synthesized BTD derivatives showed only poor or reasonable cellular selection, but with excellent fluorescence intensity and almost no background signal emitting at the blue or green channels. The knowledge gained by analysing their molecular architecture, however, allowed the planning and synthesis of a fluorescent BTD, which was then successfully tested and showed superior mitochondrial selection with outstanding results in bioimaging experiments in living cells. The new marker (named Splendor) was then compared with the commercially available MitoTracker Red (also through co-staining experiments) and showed far better mitochondrial selection, fluorescence intensity and chemical stability. Mitochondrial imaging and tracking (dynamic changes) was possible using Splendor during the whole cellular division cycle. DFT calculations were performed to offer insights into the origin of the chemical- and photostability of BTD derivatives. In addition, molecular docking calculations hint at a potential molecular target for the BTD derivatives in the mitochondrial protein adenine nucleotide translocase, which may explain the mitochondrial selectivity of Splendor versus the other four BTD derivatives.

Morita-Baylis-Hillman reaction: ESI-MS(/MS) investigation with charge tags and ionic liquid effect origin revealed by DFT calculations.

The use of a charge-tagged acrylate derivative bearing an imidazolium tag to study the Morita-Baylis-Hillman reaction via ESI-MS(/MS) monitoring and the effect of such tag (imidazolium cations and ion pairs) over TSs is described. The ionic nature of the substrate was meant to facilitate ESI transfer to the gas phase for direct mass spectrometric analysis. The detection and characterization of charged intermediates has suggested major reaction pathways. DFT calculations considering the effect of a polar and protic solvent (methanol), of a polar and aprotic solvent (acetonitrile), and of no solvent (gas phase) were used to predict possible TSs through a common accepted intermediate. The controversial proton transfer step, which may proceed via Aggarwal's or McQuade's proposals, was evaluated. Calculations predicted the formation of electrostatic intermediate complexes with both the cation and anion when charge-tagged reagents are used. These complexes contribute to the positive ionic liquid effect, and based on the formation of these unique complexes, a rationale for the ionic liquid effect is proposed. These complexes also pointed to a plausible explanation for the positive ionic liquid effect observed in several reactions that are difficult to be carried out in organic solvents but have shown a beneficial effect when performed in ionic liquids.

Facts, presumptions, and myths on the solvent-free and catalyst-free Biginelli reaction. What is catalysis for?

The current manuscript describes the role and importance of catalysis and solvent effects for the Biginelli multicomponent reaction. The overwhelming number of new catalysts and conditions recently published for the Biginelli synthesis, including in some manuscripts entitled "catalyst-free" and/or "solvent-free" have incentivized controversies and hot debates regarding the importance of developing new catalysts and reaction conditions to perform this very important multicomponent reaction. These so-called "catalyst-free" reports have generated much confusion in the field, requiring urgent elucidations. In this manuscript, we exemplify, demystify, and discuss the crucial role of catalysis, solvent effects, mechanisms, kinetics, facts, presumptions, and myths associated with the Biginelli reaction aiming to avoid current and future confusion and to stimulate new approaches.