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Updated: Oct 13, 2025

Chemoselective Modification of Viral Surfaces via Bioorthogonal Click Chemistry
Published on: August 19, 2012
In Silico Discovery of Multistep Chemistry Initiated by a Conical Intersection: The Challenging Case of
David M Sanchez1,2, Umberto Raucci1,2, Todd J Martínez1,2
1Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States.
Abstract:
Detailed mechanistic understanding of multistep chemical reactions triggered by internal conversion via a conical intersection is a challenging task that emphasizes limitations in theoretical and experimental techniques. We present a discovery-based, hypothesis-free computational approach based on first-principles molecular dynamics to discover and refine the switching mechanism of donor-acceptor Stenhouse adducts (DASAs). We simulate the photochemical experiment in silico, following the "hot" ground state dynamics for 10 ps after photoexcitation. Using state-of-the-art graphical processing units-enabled electronic structure calculations we performed in total ∼2 ns of nonadiabatic ab initio molecular dynamics discovering (a) critical intermediates that are involved in the open-to-closed transformation, (b) several competing pathways which lower the overall switching yield, and (c) key elements for future design strategies. Our dynamics describe the natural evolution of both the nuclear and electronic degrees of freedom that govern the interconversion between DASA ground-state intermediates, exposing significant elements for future design strategies of molecular switches.
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Conjugate addition results in a thermodynamically stable product. The reaction retains the stronger C=O bond at the expense of the weaker C=C π bond. The process is slow as the β carbon is less electrophilic than the carbonyl carbon.
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