I originally created this website for myself and members of Prof. Dr. Abe’s research group at Hiroshima University to take notes on quantum chemical computations. Over time, more and more people began visiting the site, and I realized that as a researcher, it’s important to contribute not only through research results but also by sharing useful resources. So, I began posting blogs and programs here that I hope others will find helpful. I hope you enjoy them!
The nucleus-independent chemical shift (NICS) criterion plays a significant role in evaluating (anti-)aromaticity. While readily accessible even for non-computational chemists, adding ghost atoms for multi-points NICS evaluations poses a significant challenge. In this article, I introduce py.Aroma, a freely available and open-source Python package designed specifically for analyzing (anti-)aromaticity. Through its user-friendly graphical interface, py.Aroma simplifies and enhances aromaticity analyses by offering key features such as HOMA/HOMER index computation, Gaussian-type input file generation for diverse NICS calculations and corresponding output processing, NMR spectra plotting, and generating computational supporting information (SI) for scientific manuscripts. Additionally, NICS⊥ is suggested for evaluating (anti-)aromaticity for non-planar or tilted rings. Pre-compiled executables for macOS and Windows are available at https://wongzit.github.io/program/pyaroma. Make facilitate accessibility for users lacking programming experience or time constraints.
@article{pyaroma2024,title={py.Aroma: An Intuitive Graphical User Interface for Diverse Aromaticity Analyses},author={Wang, Z.},journal={Chemistry},volume={6},issue={6},pages={1692--1703},year={2024},month=dec,publisher={MDPI},doi={10.3390/chemistry6060103},url={https://doi.org/10.3390/chemistry6060103},dimensions={true},google_scholar_id={eQOLeE2rZwMC},}
Long-lived localised singlet diradicaloids with carbon–carbon π-single bonding (C–π–C)
Localised singlet cyclopentane-1,3-diyl diradicaloids have been considered promising candidates for constructing carbon–carbon π-single bonds (C–π–C). However, the high reactivity during formation of the σ-bond has limited a deeper investigation of its unique chemical properties. In this feature article, recent progress in kinetic stabilisation based on the “stretch effect” and the “solvent dynamic effect” induced by the macrocyclic system is summarised. Singlet diradicaloids S-DR4a/b and S-DR4d containing macrocyclic rings showed much longer lifetimes at 293 K (14 μs for S-DR4a and 156 μs for S-DR4b in benzene) compared to the parent singlet diradicaloid S-DR2 having no macrocyclic ring (209 ns in benzene). Furthermore, the dynamic solvent effect in viscous solvents was observed for the first time in intramolecular σ-bond formation, the lifetime of S-DR4d increased to 400 μs in the viscous solvent glycerin triacetin at 293 K. The experimental results proved the validity of the “stretch effect” and the “solvent dynamic effect” on the kinetic stabilisation of singlet cyclopentane-1,3-diyl diradicaloids, and provided a strategy for isolating the carbon–carbon π-single bonded species (C–π–C), and towards a deeper understanding of the nature of chemical bonding.
@article{ccstretch2021,title={Long-lived localised singlet diradicaloids with carbon–carbon π-single bonding (C–π–C)},author={Wang, Z. and Yadav, P. and Abe, M.},journal={Chem. Commun.},volume={57},issue={86},pages={11301--11309},year={2021},month=sep,publisher={rsc},doi={10.1039/d1cc04581d},url={https://doi.org/10.1039/d1cc04581d},dimensions={true},google_scholar_id={UeHWp8X0CEIC},}
SOMO–HOMO Conversion in Triplet Cyclopentane-1,3-diyl Diradicals
According to the Aufbau principle, singly occupied molecular orbitals (SOMOs) are energetically higher lying than a highest doubly occupied molecular orbital (HOMO) in the electronically ground state of radicals. However, in the last decade, SOMO–HOMO-converted species have been reported in a limited group of radicals, such as distonic anion radicals and nitroxides. In this study, SOMO–HOMO conversion was observed in triplet 2,2-difluorocyclopentane-1,3-diyl diradicals DR3F1, DR4F1, and 2-fluorocyclopentante-1,3-diyl diradical DR3HF1, which contain the anthracyl unit at the remote position. The high HOMO energy in the anthracyl moiety and the low-lying SOMO–1 due to the fluoro-substituent effect are the key to the SOMO–HOMO conversion phenomenon. Furthermore, the cation radical DR3F1+ generated through the one-electron oxidation of DR3F1 was found to be a SOMO–HOMO-converted monoradical.
@article{shc2021,title={SOMO–HOMO Conversion in Triplet Cyclopentane-1,3-diyl Diradicals},author={Wang, Z. and Murata, R. and Abe, M.},journal={ACS Omega},volume={6},issue={35},pages={22773--22779},year={2021},month=jul,publisher={acs},doi={10.1021/acsomega.1c03125},url={https://doi.org/10.1021/acsomega.1c03125},dimensions={true},google_scholar_id={2osOgNQ5qMEC},}
Impact of the macrocyclic structure and dynamic solvent effect on the reactivity of a localised singlet diradicaloid with π-single bonding character
Z. Wang, R. Akisaka , S. Yabumoto , T. Nakagawa , S. Hatano , and M. Abe
Localised singlet diradicals are key intermediates in bond homolysis processes. Generally, these highly reactive species undergo radical–radical coupling reaction immediately after their generation. Therefore, their short-lived character hampers experimental investigations of their nature. In this study, we implemented the new concept of “stretch effect” to access a kinetically stabilised singlet diradicaloid. To this end, a macrocyclic structure was computationally designed to enable the experimental examination of a singlet diradicaloid with π-single bonding character. The kinetically stabilised diradicaloid exhibited a low carbon–carbon coupling reaction rate of 6.4 × 103 s−1 (155.9 μs), approximately 11 and 1000 times slower than those of the first generation of macrocyclic system (7.0 × 104 s−1, 14.2 μs) and the parent system lacking the macrocycle (5 × 106 s−1, 200 ns) at 293 K in benzene, respectively. In addition, a significant dynamic solvent effect was observed for the first time in intramolecular radical–radical coupling reactions in viscous solvents such as glycerin triacetate. This theoretical and experimental study demonstrates that the stretch effect and solvent viscosity play important roles in retarding the σ-bond formation process, thus enabling a thorough examination of the nature of the singlet diradicaloid and paving the way toward a deeper understanding of reactive intermediates.
@article{stretch2021,title={Impact of the macrocyclic structure and dynamic solvent effect on the reactivity of a localised singlet diradicaloid with π-single bonding character},author={Wang, Z. and Akisaka, R. and Yabumoto, S. and Nakagawa, T. and Hatano, S. and Abe, M.},journal={Chem. Sci.},volume={12},issue={2},pages={613--625},year={2021},month=jan,publisher={rsc},doi={10.1039/d0sc05311b},url={https://doi.org/10.1039/d0sc05311b},dimensions={true},google_scholar_id={u5HHmVD_uO8C},}