|
|
|
|
|
|
| Simulation and Software Development of Electronic Circular
Dichroic Spectrum |
| XU Fan2, SU Jun-kui1, WEN Yan1, GAN Li-she1, 2* |
1. School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
2. Institute of Modern Chinese Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
|
|
|
|
|
Abstract Organic small molecules, especially natural products, have complex and diverse structures and generally contain multiple chiral centers, so the determination of their absolute configuration has always been a challenge in structural elucidation. Electronic circular dichroism (ECD) is a powerful tool for identifying absolute configuration because of its concise curve and without sample loss. With effective use of computer technology and quantum chemistry theories such as density functional theory (DFT) and time-dependent density functional theory (TDDFT), the calculation of theoretical ECD spectrum and comparison with the experimental one has become a state-of-the-art technique for absolute configuration determination. The main process is as follows: First, the relative configuration of the compound needs to be determined before calculation. Conformation analyses are carried out to identify multiple lowest energy conformers, which are then subjected to geometric optimization and vibration analysis (such as the energy threshold within 2.0 kcal·mol-1). ECD-related parameters, such as electronic excitation energy (eV) and rotor strength (10-40 erg-esu-cm), are further calculated for each lowest energy conformer. Finally, these data are processed according to Gaussian broadening function for spectrum fitting, and the calculated spectrum of all conformers is averaged according to their Boltzman weight. This article mainly summarizes the simulation method of the ECD curve and the evaluation standards of the ECD calculation result. Furthermore, software was developed for automatically processing Gaussian ECD calculation results and simulation of ECD curve based on Python language. The software can locate keywords in the output files. For the geometry optimization and vibration analysis output files, it can capture the Gibbs free energy data of each conformer and weight the Boltzmann distribution. The ECD-related properties output files can capture the excitation energy (eV), the corresponding oscillator and rotatory strength, and simulate the theoretical spectrum. The software can adjust simulation parameters in real-time and compare them with the experimental curve, facilitating the data processing and result evaluation of the calculated ECD.
|
|
Received: 2022-06-06
Accepted: 2022-10-24
|
|
|
|
Corresponding Authors:
GAN Li-she
E-mail: ganlishe@163.com
|
|
[1] CHEN Yi-ping, CHEN Lian-hui（陈依萍, 陈连辉）. Technology and Development of Chemical Industry（化工技术与开发）, 2018, 47(4): 50.
[2] Berova N, Di Bari L, Pescitelli G. Chemical Society Reviews, 2007, 36(6): 914.
[3] Orio M, Pantazis D A, Neese F. Photosynthesis Research, 2009, 102(2-3): 443.
[4] Casida M E, Huix-Rotllant M. Annual Review of Physical Chemistry, 2012, 63: 287.
[5] Marques M A, Gross E K. Annual Review of Physical Chemistry, 2004, 55: 427.
[6] Fu Y F, Ding X Y, Zhang X L, et al. Journal of Natural Products, 2020, 83(4): 1229.
[7] Zhu L J, Cao F, Su X X, et al. The Journal of Organic Chemistry, 2020, 85(13): 8580.
[8] Kim D H, Kim C S, Subedi L, et al. Tetrahedron Letters, 2019, 60(41): 151130.
[9] Frisch M J, Trucks G W, Schlegel H B, et al. Gaussian 16 Rev.B.01[CP]. Wallingford, CT: 2016.
[10] Aidas K, Angeli C, Bak K, et al. Wiley Interdisciplinary Reviews—Computational Molecular Science, 2014, 4(3): 269.
[11] Bruhn T, Schaumlöffel A, Hemberger Y, et al. SpecDis version 1.71, Berlin, Germany, 2017, http://specdis-software.jimdo.com.
[12] Lu T, Chen F W. Journal of Computational Chemistry, 2012, 33: 580.
[13] Grauso L, Teta R, Esposito G, et al. Natural Product Reports, 2019, 36(7): 1005.
[14] Stephens P J, Harada N. Chirality, 2010, 22(2): 229.
[15] Yuan F Y, Xu F, Fan R Z, et al. The Journal of Organic Chemistry, 2021, 86(11): 7588.
[16] Fan Y Y, Gan L S, Chen S X, et al. The Journal of Organic Chemistry, 2021, 86(16): 11277.
[17] Xu F, Zhang L S, Zhou C X, et al. Bioorganic Chemistry, 2021, 113: 105030.
|
| [1] |
JIANG Wei-na1,2, YANG Shi-long1,3, LU Wen4, XU Li2,3,4*, TANG Ying2,3,5, XUE Hua-yu1, GAO Bu-hong3, DU Li-ting3, SUN Hai-jun3, MA Meng-tao4, XU Hai-jun1*, CAO Fu-liang2,5. Quercetin-Functionalized Core-Shell Ag@SiO2 Nanoparticles for Detection of Copper Ions[J]. SPECTROSCOPY AND SPECTRAL ANALYSIS, 2018, 38(08): 2650-2656. |
| [2] |
YANG Shi-long1, 2, JIANG Wei-na1, 2, YIN Bin3, XU Li2, 3, 4*, ZHAO Feng-yi2, 5, GAO Bu-hong4, SUN Hai-jun4, DU Li-ting4, TANG Ying4, 5, CAO Fu-liang2, 5. A Quercetin-Based Fluorescent Probe for the Recognition of Fluorid Ions[J]. SPECTROSCOPY AND SPECTRAL ANALYSIS, 2016, 36(11): 3582-3587. |
|
|
|
|
