Electronic Quantum Fluxes during Pericyclic Reactions Exemplified for the Cope Rearrangement of Semibullvalene

Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene

We show herein that 1,10-dicyano substitution restricts the paragon fluxionality of bullvalene to just 14 isomers which isomerize along a single cycle. The restricted fluxionality of 1,10-dicyanobullvalene (DCB) is investigated by means of: (i) Bonding analyses of the isomer structures using the adaptive natural density partitioning (AdNDP). (ii) Quantum dynamical simulations of the isomerizations along the cyclic intrinsic reaction coordinate of the potential energy surface (PES). The PES possesses 14 equivalent potential wells supporting 14 isomers which are separated by 14 equivalent potential barriers supporting 14 transition states. Accordingly, at low temperatures, DCB appears as a hindered molecular rotor, without any delocalization of the wavefunction in the 14 potential wells, without any nuclear spin isomers, and with completely negligible tunneling. These results are compared and found to differ from those for molecular boron rotors. (iii) Born-Oppenheimer molecular dynamics (BOMD) simulations of thermally activated isomerizations. (iv) Calculations of the rate constants in the frame of transition state theory (TST) with reasonable agreement achieved with the BOMD results. (v) Simulations of the equilibration dynamics using rate equations for the isomerizations with TST rate coefficients. Accordingly, in the long-time limit, isomerizations of the 14 isomers, each with Cs symmetry, approach the "14 Cs → C7v" thermally averaged structure. This is a superposition of the 14 equally populated isomer structures with an overall C7v symmetry. By extrapolation, the results for DCB yield working hypotheses for so far un-explored properties e.g. for the equilibration dynamics of C10H10.

Spin current in the early stage of radical reactions and its mechanisms

We study the electronic spin flux (atomic-scale flow of the spin density in molecules) by a perturbation analysis and ab initio nonadiabatic calculations. We derive a general perturbative expression of the charge and spin fluxes and identify the driving perturbation of the fluxes to be the time derivative of the electron-nucleus interaction term in the Hamiltonian. We then expand the expression in molecular orbitals so as to identify relevant components of the fluxes. Our perturbation theory describes the electronic fluxes in the early stage of reactions in an intuitively clear manner. The perturbation theory is then applied to an analysis of the spin flux obtained in ab initio calculations of the radical reaction of O2 and CH3· starting from three distinct spin configurations; (a) CH3· and triplet O2 with total spin of the system set Stot=1/2 (b) CH3· and singlet O2, Stot=1/2, and (c) CH3· and triplet O2, Stot=3/2. Further analysis of the time-dependent behaviors of the spin flux in these numerical simulations reveals (i) the spin flux induces rearrangement of the local spin structure, such as reduction of the spin polarization arising from the triplet O2 and (ii) the spin flux flows from O2 to CH3· in the reaction starting from spin configuration (a) and from CH3· to O2 in that starting from configuration (b), whereas no major intermolecular spin flux was observed in that starting from configuration (c). Our study thus establishes the mechanism of the spin flux that rearranges the local spin structures associated with chemical bonds.

Curly arrows, electron flow, and reaction mechanisms from the perspective of the bonding evolution theory

Despite the usefulness of curly arrows in chemistry, their relationship with real electron density flows is still imprecise, and even their direct connection to quantum chemistry is still controversial. The paradigmatic description - from first principles - of the mechanistic aspects of a given chemical process is based mainly on the relative energies and geometrical changes at the stationary points of the potential energy surface along the reaction pathway; however, it is not sufficient to describe chemical systems in terms of bonding aspects. Probing the electron density distribution during a chemical reaction can provide important insights, enabling us to understand and control chemical reactions. This aim has required an extension of the relationships between the concepts of traditional chemistry and those of quantum mechanics. Bonding evolution theory (BET), which combines the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT), provides a powerful method that offers insight into the molecular mechanism of chemical rearrangements. In agreement with the laws of physical and aspects of quantum theory, BET can be considered an appropriate tool to tackle chemical reactivity with a wide range of possible applications. In this work, BET is applied to address a long-standing problem: the ability to monitor the flow of electron density. BET analysis shows a connection between quantum mechanics and bond making/forming processes. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds and provides detailed physical grounds for this type of representation. We demonstrate this procedure using the test set of prototypical examples of thermal ring apertures, and the degenerated Cope rearrangement of semibullvalene.

Concerted Electronic and Nuclear Fluxes During Coherent Tunnelling in Asymmetric Double-Well Potentials

The quantum theory of concerted electronic and nuclear fluxes (CENFs) during coherent periodic tunnelling from reactants (R) to products (P) and back to R in molecules with asymmetric double-well potentials is developed. The results are deduced from the solution of the time-dependent Schrödinger equation as a coherent superposition of two eigenstates; here, these are the two states of the lowest tunnelling doublet. This allows the periodic time evolutions of the resulting electronic and nuclear probability densities (EPDs and NPDs) as well as the CENFs to be expressed in terms of simple sinusodial functions. These analytical results reveal various phenomena during coherent tunnelling in asymmetric double-well potentials, e.g., all EPDs and NPDs as well as all CENFs are synchronous. Distortion of the symmetric reference to a system with an asymmetric double-well potential breaks the spatial symmetry of the EPDs and NPDs, but, surprisingly, the symmetry of the CENFs is conserved. Exemplary application to the Cope rearrangement of semibullvalene shows that tunnelling of the ideal symmetric system can be suppressed by asymmetries induced by rather small external electric fields. The amplitude for the half tunnelling, half nontunnelling border is as low as 0.218 × 10(-8) V/cm. At the same time, the delocalized eigenstates of the symmetric reference, which can be regarded as Schrödinger's cat-type states representing R and P with equal probabilities, get localized at one or the other minima of the asymmetric double-well potential, representing either R or P.

Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.

Staircase patterns of nuclear fluxes during coherent tunneling in excited doublets of symmetric double well potentials

Step-by-step flux for one-by-one transfers of the lobes of the density, from the reactant (left) to the product (right) in the excited tunneling doublet.

Quantum theory of concerted electronic and nuclear fluxes associated with adiabatic intramolecular processes

Example of concerted electronic (right) and nuclear (left) fluxes: isomerization of B₄.

X-ray imaging of chemically active valence electrons during a pericyclic reaction

Time-resolved imaging of chemically active valence electron densities is a long-sought goal, as these electrons dictate the course of chemical reactions. However, X-ray scattering is always dominated by the core and inert valence electrons, making time-resolved X-ray imaging of chemically active valence electron densities extremely challenging. Here we demonstrate an effective and robust method, which emphasizes the information encoded in weakly scattered photons, to image chemically active valence electron densities. The degenerate Cope rearrangement of semibullvalene, a pericyclic reaction, is used as an example to visually illustrate our approach. Our work also provides experimental access to the long-standing problem of synchronous versus asynchronous bond formation and breaking during pericyclic reactions.

X-ray scattering experiments give details of the electrons in a system, although typically this is dominated by core and inert valence electrons. Here, the authors report a method to follow changes in the chemically active valence electrons, and use it to study the reaction mechanism of a pericyclic reaction.

How a Quantum Chemical Topology Analysis Enables Prediction of Electron Density Transfers in Chemical Reactions. The Degenerated Cope Rearrangement of Semibullvalene

Recent works on the reaction mechanism for the degenerated Cope rearrangement (DCR) of semibullvalene (SBV) in the ground state prompted us to investigate this complex rearrangement in order to assign experimentally observed contrast features in the simulated electron distribution. We present a joint use of the electron localization function (ELF) and Thom's catastrophe theory (CT) as a powerful tool to analyze the electron density transfers along the DCR. The progress of the reaction is monitored by the structural stability domains of the topology of ELF, while the change between them is controlled by turning points derived from CT. The ELF topological analysis shows that the DCR of SBV corresponds to asynchronous electron density rearrangement taking place in three consecutive stages. We show how the pictures anticipated by drawing Lewis structures of the rearrangement correlate with the experimental data and time-dependent quantum description of the process.