Testing the Simplified Molecular Dynamics Approach to Improve the Reproduction of ECD Spectra and Monitor Aggregation
A simplified molecular-dynamics-based electronic circular dichroism (ECD) approach was tested on three condensed derivatives with limited conformational flexibility and an isochroman-2H-chromene hybrid, the ECD spectra of which could not be precisely reproduced by the conventional ECD calculation pr...
Elmentve itt :
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| Dokumentumtípus: | Cikk |
| Megjelent: |
2024
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| Sorozat: | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
25 No. 12 |
| Tárgyszavak: | |
| doi: | 10.3390/ijms25126453 |
| mtmt: | 34999575 |
| Online Access: | http://publicatio.bibl.u-szeged.hu/33079 |
| LEADER | 02364nab a2200349 i 4500 | ||
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| 005 | 20240613100702.0 | ||
| 008 | 240613s2024 hu o 000 eng d | ||
| 022 | |a 1661-6596 | ||
| 024 | 7 | |a 10.3390/ijms25126453 |2 doi | |
| 024 | 7 | |a 34999575 |2 mtmt | |
| 040 | |a SZTE Publicatio Repozitórium |b hun | ||
| 041 | |a eng | ||
| 100 | 1 | |a Mándi Attila | |
| 245 | 1 | 0 | |a Testing the Simplified Molecular Dynamics Approach to Improve the Reproduction of ECD Spectra and Monitor Aggregation |h [elektronikus dokumentum] / |c Mándi Attila |
| 260 | |c 2024 | ||
| 300 | |a 18 | ||
| 490 | 0 | |a INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES |v 25 No. 12 | |
| 520 | 3 | |a A simplified molecular-dynamics-based electronic circular dichroism (ECD) approach was tested on three condensed derivatives with limited conformational flexibility and an isochroman-2H-chromene hybrid, the ECD spectra of which could not be precisely reproduced by the conventional ECD calculation protocol. Application of explicit solvent molecules at the molecular mechanics (MD) level in the dynamics simulations and subsequent TDDFT-ECD calculation for the unoptimized MD structures was able to improve the agreements between experimental and computed spectra. Since enhancements were achieved even for molecules with limited conformational flexibility, deformations caused by the solvent molecules and multitudes of conformers produced with unoptimized geometries seem to be key factors for better agreement. The MD approach could confirm that aggregation of the phenanthrene natural product luzulin A had a significant contribution to a specific wavelength range of the experimental ECD. The MD approach has proved that dimer formation occurred in solution and this was responsible for the anomalous ECD spectrum. The scope and limitations of the method have also been discussed. | |
| 650 | 4 | |a Kémiai tudományok | |
| 650 | 4 | |a Általános orvostudomány | |
| 700 | 0 | 1 | |a Rimóczi Aliz |e aut |
| 700 | 0 | 1 | |a Vasas Andrea |e aut |
| 700 | 0 | 1 | |a Hohmann Judit |e aut |
| 700 | 0 | 1 | |a Swamy Mahadeva M. M. |e aut |
| 700 | 0 | 1 | |a Monde Kenji |e aut |
| 700 | 0 | 1 | |a Barta Roland A. |e aut |
| 700 | 0 | 1 | |a Kicsák Máté |e aut |
| 700 | 0 | 1 | |a Komáromi István |e aut |
| 700 | 0 | 1 | |a Fehér Krisztina |e aut |
| 700 | 0 | 1 | |a Kurtán Tibor |e aut |
| 856 | 4 | 0 | |u http://publicatio.bibl.u-szeged.hu/33079/1/ijms-25-06453.pdf |z Dokumentum-elérés |