Ultra-Fast Computation of Excited-States Spectra for Large Systems: Ultraviolet and Fluorescence Spectra of Proteins
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ORIGINAL RESEARCH ARTICLE
Ultra‑Fast Computation of Excited‑States Spectra for Large Systems: Ultraviolet and Fluorescence Spectra of Proteins Yonggang Liu1,5 · Jianjie Xu2 · Li Han3 · Qiangqiang Liu4 · Yunfan Yang5 · Zeren Li6 · Zhongyuan Lu5 · Hang Zhang6 · Tengxiao Guo2 · Qiao Liu6 Received: 18 August 2020 / Revised: 4 October 2020 / Accepted: 29 October 2020 © International Association of Scientists in the Interdisciplinary Areas 2020
Abstract A workable approach named xTB-sTDDFT was selected to investigate the excited-state spectra of oxytocin (135 atoms), GHRP-6 (120 atoms) and insulin (793 atoms). Three different Hartree–Fock components functionals (wB97XD3: 51%, LCBLYP: 53%, wB97X: 57%) were used to calculate the excitation spectra, and the results calculated by wB97XD3 functional well agree with the experiments. It’s a deep impression that computed time cost reduced by more than 80%. For polypeptide (oxytocin and GHRP-6), both UV and fluorescence spectra were obtained, and the errors between the calculated and experimental values approximately were 20 nm. For Insulin, the errors are within 15 nm. UV spectrum peak is λcal = 262 nm (λexp = 277 nm, Δλ = 15 nm), and fluorescence spectrum peak is λcal = 294 nm (λexp = 304 nm, Δλ = 10 nm). In summary, a suitable theoretical model is established to ultra-fast calculate the electronic excitation spectra of large systems, such as proteins and biomacromolecules, with good calculation accuracy, fast calculation speed and low cost.
* Yonggang Liu [email protected] * Zhongyuan Lu [email protected] 1
Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621010, China
2
State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
3
Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 102205, China
4
School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong 643000, China
5
State Key Laboratory of Environment‑Friendly Energy Materials, Southwest University of Science and Technology, Mianyang 621010, China
6
National Key Laboratory for Shock Wave and Detonation Physics, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621010, China
13
Vol.:(0123456789)
Interdisciplinary Sciences: Computational Life Sciences
Graphic abstract
Keywords Excitation spectra · Excited state · xTB · sTDDF
1 1. Introduction With the development of biotechnology, protein and polypeptide drugs have been more and more used in the treatment of diseases. To identify their molecule structure and understand their transport, metabolism process, and reaction process in the body from the molecular level, many detection methods have been applied, including immunoassay analysis [1], chromatography analysis [2], electrochemical analysis [3, 4] and spectroscopy analysis [5, 6], etc.. Because of its high sensitivity, high selectivity and small sample size, spectroscopy analysis has become one of the most important means to investigate the i
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