UV induced proton transfer in thioacetamide: first observation of thiol form of simple thioamideElectronic supplementary information (ESI): Tables S1 and S2 provide internal coordinates used in the normal mode analysis for the thione and thiol tautomers of thioacetamide. Atom numbering is given in Scheme S1. Infrared spectra of thioacetamide isolated in N2 and Ar matrices are compared in Figs. S1 and S2 with the spectra theoretically predicted at the DFT level. Table S3 provides the assignment of the bands observed in the IR spectra of thioacetamide (thione form) isolated in Ar and N2 matrices. The theoretically calculated spectra of four conformers of thioacetamide in the thiol tautomeric form are presented in Tables S4–S7. Optimised geometries of thioacetamide isomers are given in Table S8 and the relative energies calculated for these isomers are presented in Table S9. See http://www.rsc.org/suppdata/cp/b3/b300793f/

2003 ◽  
Vol 5 (8) ◽  
pp. 1524-1529 ◽  
Author(s):  
Leszek Lapinski ◽  
Hanna Rostkowska ◽  
Artem Khvorostov ◽  
Maciej J. Nowak
Author(s):  
Miquel Huix-Rotllant ◽  
Karno Schwinn ◽  
Nicolas Ferré

Combined QM/MM Hessians and local normal mode analysis are powerful tools to simulate and interpret complex IR spectra of biological macromolecules.


2011 ◽  
Vol 27 (20) ◽  
pp. 2843-2850 ◽  
Author(s):  
José Ramón Lopéz-Blanco ◽  
José Ignacio Garzón ◽  
Pablo Chacón

2003 ◽  
Vol 24 (7) ◽  
pp. 826-841 ◽  
Author(s):  
Kenshu Kamiya ◽  
Yoko Sugawara ◽  
Hideaki Umeyama

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0258818
Author(s):  
Byung Ho Lee ◽  
Soon Woo Park ◽  
Soojin Jo ◽  
Moon Ki Kim

Large-scale conformational changes are essential for proteins to function properly. Given that these transition events rarely occur, however, it is challenging to comprehend their underlying mechanisms through experimental and theoretical approaches. In this study, we propose a new computational methodology called internal coordinate normal mode-guided elastic network interpolation (ICONGENI) to predict conformational transition pathways in proteins. Its basic approach is to sample intermediate conformations by interpolating the interatomic distance between two end-point conformations with the degrees of freedom constrained by the low-frequency dynamics afforded by normal mode analysis in internal coordinates. For validation of ICONGENI, it is applied to proteins that undergo open-closed transitions, and the simulation results (i.e., simulated transition pathways) are compared with those of another technique, to demonstrate that ICONGENI can explore highly reliable pathways in terms of thermal and chemical stability. Furthermore, we generate an ensemble of transition pathways through ICONGENI and investigate the possibility of using this method to reveal the transition mechanisms even when there are unknown metastable states on rough energy landscapes.


2016 ◽  
Vol 24 (20) ◽  
pp. 4855-4866 ◽  
Author(s):  
Victor A. Gil ◽  
Daniel Lecina ◽  
Christoph Grebner ◽  
Victor Guallar

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