36 research outputs found
Interactive Chemical Reactivity Exploration
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
transition-state 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.Comment: 36 pages, 14 figure
Studying chemical reactivity in a virtual environment
Chemical reactivity of a set of reactants is determined by its potential (electronic) energy (hyper)surface. The high dimensionality of this surface renders it difficult to efficiently explore reactivity in a large reactive system. Exhaustive sampling techniques and search algorithms are not straightforward to employ as it is not clear which explored path will eventually produce the minimum energy path of a reaction passing through a transition structure. Here, the chemist's intuition would be of invaluable help, but it cannot be easily exploited because (1) no intuitive and direct tool for the scientist to manipulate molecular structures is currently available and because (2) quantum chemical calculations are inherently expensive in terms of computational effort. In this work, we elaborate on how the chemist can be reintroduced into the exploratory process within a virtual environment that provides immediate feedback and intuitive tools to manipulate a reactive system. We work out in detail how this immersion should take place. We provide an analysis of modern semi-empirical methods which already today are candidates for the interactive study of chemical reactivity. Implications of manual structure manipulations for their physical meaning and chemical relevance are carefully analysed in order to provide sound theoretical foundations for the interpretation of the interactive reactivity exploration.ISSN:1359-6640ISSN:1364-549
Integrated Reaction Path Processing from Sampled Structure Sequences
Sampled structure
sequences obtained, for instance, from real-time
reactivity explorations or first-principles molecular dynamics simulations
contain valuable information about chemical reactivity. Eventually,
such sequences allow for the construction of reaction networks that
are required for the kinetic analysis of chemical systems. For this
purpose, however, the sampled information must be processed to obtain
stable chemical structures and associated transition states. The manual
extraction of valuable information from such reaction paths is straightforward
but unfeasible for large and complex reaction networks. For real-time
quantum chemistry, this implies automatization of the extraction and
relaxation process while maintaining immersion in the virtual chemical
environment. Here, we describe an efficient path processing scheme
for the on-the-fly construction of an exploration network by approximating
the explored paths as continuous basis-spline curves