Interactive Chemical Reactivity Exploration

Abstract

Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transitionstate structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We employ a haptic pointer device with force-feedback to allow the operator the direct manipulation of structures in three dimensions along with simultaneous perception of the quantum mechanical response upon structure modification as forces. We elaborate on the details of how such an interactive exploration should proceed and which technical difficulties need to be overcome. All reactivity-exploration concepts developed for this purpose have been implemented in the Samson programming environment.

Real-time feedback from iterative electronic structure calculations

“…We extended our real‐time quantum chemistry framework within the SAMSON molecular editor to reactivity studies based on iterative electronic structure methods. As SCF methods, we implemented the semiempirical Parametrized Method 6 (PM6) and self‐consistent DFTB variants .…”

“…Recently, we demonstrated the application of real‐time reactivity studies described by the nonself‐consistent density‐functional tight‐binding (DFTB) method . DFTB is a noniterative method featuring constant execution times, and therefore, delivers forces at a constant frequency.…”

Mode‐tracking based stationary‐point optimization

“…Clearly, this requires the (desirable) interference of an operator with the search procedure, which is simply a matter of efficient software design (similar operator friendliness was already accomplished in the Mode‐Tracking set‐up tool). For instance, it is possible to supply more information about the transition path direction to MTsearch than only the first eigenvector (e.g., a sequence of structures which can for example easily be generated by a haptic device). The guess vectors for the first few Mode‐Tracking calculations are then chosen according to the predefined sequence of structures.…”

“…Moreover, a feature of our approach is that the initial molecular distortion to be followed can be set up in a very general way to accommodate chemical insight into the system under study. Hence, interference by the operator who launched the search is a desired feature for the exploration of chemical reactions in complex systems, especially if this can be done in an interactive manner with methods based on real‐time quantum chemistry …”

Visualization of Biomolecular Structures: State of the Art Revisited

“…A typical setup is depicted in Figure . Nowadays, even chemical reactivity can be explored interactively using QM simulations [HVB*14, LJM15]. Such interactive experiments are facilitated by visual manipulation guides discussed by Kreylos et al .…”