Theoretical Studies of Furan and Thiophene Nanothreads: Structures, Cycloaddition Barriers, and Activation Volumes

Bond Lengths and Dipole Moments of Diatomic Molecules under Isotropic Pressure with the XP-PCM and GOSTSHYP Models

While high-pressure chemistry has a well-established history, methods to simulate pressure at the single-molecule level have been somewhat lacking. The current work aims at comparing two static models (XP-PCM and GOSTSHYP) to apply isotropic pressure to single molecules, focusing on the equilibrium bond length and electric dipole moment of diatomic molecules. Numerical challenges arising in the potential energy surface using the XP-PCM method were examined, and a pragmatic approach was followed to mitigate these. The definition of the cavity was scrutinized, and two approaches to retrieve the isotropic character that could potentially be lost when using the standard methodology were suggested. Subsequently, equilibrium bond lengths under pressure were evaluated, showing reasonable agreement between GOSTSHYP and XP-PCM, but some discrepancies persist. A Taylor series analysis introduced elsewhere was then applied to rationalize the observed trends in terms of the bond surface. Finally, the dipole moment was shown to be highly sensitive to the cavity definition, and qualitative agreement necessitates the use of our adapted procedure.

Prediction of a Novel Electromechanical Response in Polar Polymers with Rigid Backbones: Contrasting Furan-Derived Nanothreads to Poly(Vinylidene Fluoride)

Syn furan nanothreads have all oxygen atoms arranged on one side of the thread backbone; these polar threads present intriguing opportunities in electromechanical response owing to their rigid ladder-like backbone. We retrained a C/H/O reactive force field to simulate their response to external electric field for both end-anchored individual threads and bulk nanothread crystals, contrasting the results to those for poly(vinylidene fluoride) (PVDF) polymer. Whereas the field induces a length-independent torque in PVDF through backbone rotation about σ bonds, furan-derived nanothreads generate a length-dependent torque by progressively twisting their rigid backbone. This mode of response couples the rotational history of the electric field to axial tension in the anchored thread. In simulations of densely packed syn furan nanothread crystals without anchors, the crystals pole in a field (∼3 GV/m at 300 K) similar to that seen in simulations of PVDF, suggesting that crystals of polar nanothreads can be ferroelectric.

Activation volume and quantum tunneling in the hydrogen transfer reaction between methyl radical and methane: A first computational study

We present a theory of the effect of quantum tunneling on the basic parameter that characterizes the effect of pressure on the rate constant of chemical reactions in a dense phase, the activation volume. This theory results in combining, on the one hand, the extreme pressure polarizable continuum model, a quantum chemical method to describe the effect of pressure on the reaction energy profile in a dense medium, and, on the other hand, the semiclassical version of the transition state theory, which includes the effect of quantum tunneling through a transmission coefficient. The theory has been applied to the study of the activation volume of the model reaction of hydrogen transfer between methyl radical and methane, including the primary isotope substitution of hydrogen with deuterium (H/D). The analysis of the numerical results offers, for the first time, a clear insight into the effect of quantum tunneling on the activation volume for this hydrogen transfer reaction: this effect results from the different influences that pressure has on the competing thermal and tunneling reaction mechanisms. Furthermore, the computed kinetic isotope effect (H/D) on the activation volume for this model hydrogen transfer correlates well with the experimental data for more complex hydrogen transfer reactions.

Two-Legged Molecular Walker and Curvature: Mechanochemical Ring Migration on Graphene

Attaining controllable molecular motion at the nanoscale can be beneficial for multiple reasons, spanning from optoelectronics to catalysis. Here we study the movement of a two-legged molecular walker by modeling the migration of a phenyl aziridine ring on curved graphene. We find that directional ring migration can be attained on graphene in the cases of both 1D (wrinkled/rippled) and 2D (bubble-shaped) curvature. Using a descriptor approach based on graphene's frontier orbital orientation, we can understand the changes in binding energy of the ring as it translates across different sites with variable curvature and the kinetic barriers associated with ring migration. Additionally, we show that the extent of covalent bonding between graphene and the molecule at different sites directly controls the binding energy gradient, propelling molecular migration. Importantly, one can envision such walkers as carriers of charge and disruptors of local bonding. This study enables a new way to tune the electronic structure of two-dimensional materials for a range of applications.

Molecular Dynamics Calculations of Partial Molar Volumes of Amino Acids in Aqueous Solutions

Partial molar volumes of amino acids in their zwitterionic and molecular forms have been calculated using molecular dynamics simulations of these systems in aqueous solutions. Calculations performed with the TIP4P, SPC (rigid and flexible), SPC/E, and polarizable water models show that the choice of water model can have a significant impact on the calculated volumes. The effect of treatment of long-range electrostatic interactions on the calculated results was also investigated. Volumes obtained in simulations with a properly chosen water model fit well the experimental data for both molecular and zwitterionic forms of amino acids.