Cycloaddition reactions via "on water" protocol reactions: A density functional theory study.

In this work, the reactions of quadricyclane with dimethyl azodicarboxylate (DMAD) and of quadricyclane with diethyl azodicarboxylate (DEAD) in gas phase and in water environments were studied by a first-principles investigation within the framework of auxiliary density functional theory (ADFT). For these type of organic reactions is known that water is required to accelerate them. Since the reason of why this occur is still unknown, this work aims to gain insight into this reaction mechanism. For this investigation, the generalized gradient approximation as well as a hybrid functional were employed. The obtained optimized structures for the reactants, of the products and of the transition states are reported, together with the corresponding frequency analysis results and the reaction profiles. Along the proposed concerted reaction mechanism, a critical points search of the electron density and a charge analysis were performed. The calculated potential energy barriers of these reactions in gas phase and in water environments are compared. In agreement with experiment, the obtained results indicate that both reactions occur faster in water than in gas phase. This study shows that there is a change in the polarity of the two most important carbon atoms of the formed compounds along the reactions and that the decrease of the activation energy barrier which occurs in liquid phase in these reactions is because the structures of the main transition states are stabilized by the water environment. Therefore, the here obtained results demonstrate the important role played by the water-molecule framework into the activation energy barrier and structures of the molecules that participate in the DMAD and DEAD cycloaddition reactions.

Cartesian constraints in QM/MM optimizations.

With the rise of quantum mechanical/molecular mechanical (QM/MM) methods, the interest in the calculation of molecular assemblies has increased considerably. The structures and dynamics of such assemblies are usually governed to a large extend by intermolecular interactions. As a result, the corresponding potential energy surfaces are topological rich and possess many shallow minima. Therefore, local structure optimizations of QM/MM molecular assemblies can be challenging, in particular if optimization constraints are imposed. To overcome this problem, structure optimization in normal coordinate space is advocated. To do so, the external degrees of freedom of a molecule are separated from the internal ones by a projector matrix in the space of the Cartesian coordinates. Here we extend this approach to Cartesian constraints. To this end, we devise an algorithm that adds the Cartesian constraints directly to the projector matrix and in this way eliminates them from the reduced coordinate space in which the molecule is optimized. To analyze the performance and stability of the constrained optimization algorithm in normal coordinate space, we present constrained minimizations of small molecular systems and amino acids in gas phase as well as water employing QM/MM constrained optimizations. All calculations are performed in the framework of auxiliary density functional theory as implemented in the program deMon2k.

Isomerization Reactions of the Cu15V+ Cluster: A Density Functional Theory Study.

The investigation of the chemical reactivity of complex systems such as transition metal clusters is a very complicated task because often the structures of the corresponding transition states are far from being intuitive. Bimetallic transition metal clusters represent a particular class of complex systems. In this work, density functional theory (DFT) is applied to study the isomerization reactions of the Cu15V+ cluster. Full geometry optimizations of dozens of initial structures taken along Born-Oppenheimer molecular dynamics (BOMD) trajectories were performed using a quasi-Newton method in a reduced space Cartesian coordinate system that works considering the internal degrees of freedom. Harmonic frequencies calculations were performed at the optimized structures. To study the isomerization reactions between the obtained stable isomers, a hierarchical transition state algorithm has been applied to locate the transition states of this cluster. The found transition states were than connected with the corresponding minimum structures by calculating the intrinsic reaction coordinates. This work demonstrates the capability of the applied method to study non-intuitive rearrangement mechanisms in complex finite systems and to create networks between minima and transition state structures on their potential energy surface.