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.

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).

Selective endocytic trafficking in live cells with fluorescent naphthoxazoles and their boron complexes.

Fluorescent naphthoxazoles and their boron derivatives have been synthesized and applied as superior and selective probes for endocytic pathway tracking in live cancer cells. The best fluorophores were compared with the commercially available acridine orange (co-staining experiments), showing far better selectivity.

Synthesis, characterization, and computational study of a new dimethoxy-chalcone.

Chalcones are an important class of medicinal compounds and are known for taking part in various biological activities as in anti-inflammatory, anti-leishmania, antimitotic, and antiviral. Chemically, chalcones consist of open-chain flavonoids in which the two aromatic rings are joined by a three-carbon α,ß-unsaturated carbonyl system. The wide action spectrum has attracted our attention to synthesize, crystallize, and characterize the dimethoxy-chalcone C18H18O3. Aiming to understand the process of crystal lattice stabilization, a combination of technique has been used including X-ray diffraction, infrared spectroscopy and computational molecular modeling. The theoretical calculations were carried out by the density functional method (DFT) with the M06-2X functional, with the 6-311+G(d,p) basis set. The vibrational wavenumbers were calculated and the scaled values were compared with experimental FT-IR spectrum. The intermolecular interactions were quantified and intercontacts in the crystal structure were analyzed using Hirshfeld surfaces. Bond distances and angles described by the X-ray diffraction and theoretical calculation are very similar. The C-H….O contacts contributing to assemble the supramolecular architecture are also responsible for the molecular structure assembly.

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.

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.

Theoretical investigation on ruthenium tetraazaporphyrin as potential nitric oxide carrier in biological systems.

Nitric oxide (NO) is an important chemical compound involved in many physiological and pathological processes in living organisms. However, nitric oxide is a very reactive radical that needs to be carried through organisms to reach the desired biological target. With the aim of developing new compounds that can be used as biomedical NO carrier agents we carried out a theoretical investigation at B3LYP/6-31+G(d)/LANL2DZ level on the interaction of NO with RuTAP (Ruthenium tetraazaporphyrin) and Ru(L)TAP, where L=Cl-, NH3, and Pyridine (Py)) and the oxidation state of Ru ranging from +1 to +3. The theoretical calculation results show that the geometric and electronic parameters of the Ru-NO bond are highly dependent on the oxidation state of Ru and of the chemical nature of ligand L at axial position. The results also show clearly that RuTAP and Ru(L)TAP are good potential candidates to be used as NO carriers in living organisms.

Fully relativistic rovibrational energies and spectroscopic constants of the lowest X:(1)0(+)g, A':(1)2( u ), A:(1)1 ( u ), B':(1)0(-)u and B:(1)0(+)u states of molecular chlorine.

The main goal of this paper is to present the rovibrational energies and spectroscopic constants of the Cl(2) molecular system in the relativistic states [Formula: see text], A':(1)2( u ), A:(1)1( u ), [Formula: see text] and [Formula: see text]. More precisely, we have evaluated the Cl(2) ω ( e ), ω ( e ) x ( e ), ω ( e ) y ( e ), α ( e ), γ ( e ) and B ( e ) rovibrational spectroscopic constants using two different procedures. The first was obtained by combining the rovibrational energies, calculated through solving Schrödinger's nuclear equation and the diatomic rovibrational energy equation. The second was obtained by using the Dunham method. The calculated properties are in good agreement with available experimental data.

Theoretical investigation of nitric oxide interaction with aluminum phthalocyanine.

Nitric oxide (NO) is an extremely toxic compound formed during combustion, predominantly at high temperatures, and it is among the most important atmospheric pollutants. However, this compound has interesting biological activities, since it can control important biological processes in living organisms. With the aim of developing new materials that can be used as selective chemical sensors or as biomedical NO delivery agents we carried out a quantum mechanical study of the interaction of NO with aluminum phthalocyanine (AlPc) at B3LYP/6-31G* level. The calculation results show clearly that the complexation of NO with AlPc depends on the latter's oxidation state. NO is more strongly bonded to AlPc in the reduced state (-33.77 kcal/mol) than in the oxidized state (-4.96 kcal/mol). By applying the Fukui function and analysis of the Frontier molecular orbital, it was possible to explain the situation within which nitric oxide interacts with AlPc.