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Conformational isomers or conformers of molecules play a decisive role in chemistry and biology. However, experimental methods to investigate chemical reaction dynamics are typically not conformer-sensitive. Here, we report on a gas-phase megaelectronvolt ultrafast electron diffraction investigation of {alpha}-phellandrene undergoing an electrocyclic ring-opening reaction. We directly image the evolution of a specific set of {alpha}-phellandrene conformers into the product isomer predicted by the Woodward-Hoffmann rules in real space and time. Our experimental results are in quantitative agreement with nonadiabatic quantum molecular dynamics simulations, which provide unprecedented detail of how conformation influences time scale and quantum efficiency of photoinduced ring-opening reactions. Due to the prevalence of large numbers of conformers in organic chemistry, our findings impact our general understanding of reaction dynamics in chemistry and biology.
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We establish that matter-wave interference at near-resonant ultraviolet optical gratings can be used to spatially separate individual conformers of complex molecules. Our calculations show that the conformational purity of the prepared beam can be close to 100% and that all molecules remain in their electronic ground state. The proposed technique is independent of the dipole moment and the spin of the molecule and thus paves the way for structure-sensitive experiments with hydrocarbons and biomolecules, such as neurotransmitters and hormones, which evaded conformer-pure isolation so far
We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In particular, poly-nuclear transition metal complexes and clusters can be considered. Structural information is encoded as a graph. Stereocenter configurations are interpretable from Cartesian coordinates into an abstract index of permutation for an extensible set of polyhedral shapes. Substituents are distinguished through a ranking algorithm. Graph and stereocenter representations are freely modifiable and chiral state is propagated where possible through incurred ranking changes. Conformers are generated with full stereoisomer control by four spatial dimension Distance Geometry with a refinement error function including dihedral terms. Molecules are comparable by an extended graph isomorphism and their representation is canonicalizeable. Molassembler is written in C++ and provides Python bindings.
Most of current neural network models in quantum chemistry (QC) exclude the molecular symmetry, separate the well-correlated real space (R space), and momenta space (K space) into two individuals, which lack the essential physics in molecular chemistry. In this work, by endorsing the molecular symmetry and elementals of group theory, we propose a comprehensive method to apply symmetry in the graph neural network (SY-GNN), which extends the property-predicting coverage to all the orbital symmetry for both ground and excited states. SY-GNN shows excellent performance in predicting both the absolute and relative of R and K spaces quantities. Besides the numerical properties, SY-GNN also can predict the orbitals distributions in real space, providing the active regions of chemical reactions. We believe the symmetry endorsed deep learning scheme covers the significant physics inside and is essential for the application of neural networks in QC and many other research fields in the future.
Perfectly controlled molecules are at the forefront of the quest to explore chemical reactivity at ultra low temperatures. Here, we investigate for the first time the formation of the long-lived intermediates in the time-dependent scattering of cold bialkali $^{23}$Na$^{87}$Rb molecules with and without the presence of infrared trapping light. During the nearly 50 nanoseconds mean collision time of the intermediate complex, we observe unconventional roaming when for a few tens of picoseconds either NaRb or Na$_2$ and Rb$_2$ molecules with large relative separation are formed before returning to the four-atom complex. We also determine the likelihood of molecular loss when the trapping laser is present during the collision. We find that at a wavelength of 1064 nm the Na$_2$Rb$_2$ complex is quickly destroyed and thus that the $^{23}$Na$^{87}$Rb molecules are rapidly lost.
On NaCl(100)/Cu(111) an interface state band is observed that descends from the surface-state band of the clean copper surface. This band exhibits a Moire-pattern-induced one-dimensional band gap, which is accompanied by strong standing-wave patterns, as revealed in low-temperature scanning tunneling microscopy images. At NaCl island step edges, one can directly see the refraction of these standing waves, which obey Snells refraction law.
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