Quasi-Particle Approach to 2D IR Spectra of Vibrational Excitons in Biomolecules: Molecular Dynamics versus Stochastic Simulation Protocols

2013 ◽  
pp. 418-449
2013 ◽  
Vol 139 (5) ◽  
pp. 054506 ◽  
Author(s):  
Myung Won Lee ◽  
Joshua K. Carr ◽  
Michael Göllner ◽  
Peter Hamm ◽  
Markus Meuwly

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2685 ◽  
Author(s):  
Weihua Wang ◽  
Wenling Feng ◽  
Wenliang Wang ◽  
Ping Li

To explore the potential reactivity of the methylidyne radical (CH) toward 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the reaction mechanism between them has been systematically investigated employing the density functional theory (DFT) and ab initio molecular dynamics simulations. The relevant thermodynamic and kinetic parameters in the possible reaction pathways have been discussed as well as the IR spectra and hyperfine coupling constants (hfcc’s) of the major products. Different from the reaction of the CH radical with 2,3,7,8-tetrachlorodibenzofuran, CH radical can attack all the C-C bonds of TCDD to form an initial intermediate barrierlessly via the cycloaddition mechanism. After then, the introduced C-H bond can be further inserted into the C-C bond of TCDD, resulting in the formation of a seven-membered ring structure. The whole reactions are favorable thermodynamically and kinetically. Moreover, the major products have been verified by ab initio molecular dynamics simulations. The distinct IR spectra and hyperfine coupling constants of the major products can provide some help for their experimental detection and identification. In addition, the reactivity of the CH radical toward the F- and Br-substituted TCDDs has also been investigated. Hopefully, the present findings can provide new insights into the reactivity of the CH radical in the transformation of TCDD-like dioxins.


2009 ◽  
Vol 113 (35) ◽  
pp. 12037-12049 ◽  
Author(s):  
Neelanjana Sengupta ◽  
Hiroaki Maekawa ◽  
Wei Zhuang ◽  
Claudio Toniolo ◽  
Shaul Mukamel ◽  
...  

2019 ◽  
Vol 21 (18) ◽  
pp. 9433-9440 ◽  
Author(s):  
Rafael Escribano ◽  
Pedro C. Gómez ◽  
Belén Maté ◽  
Germán Molpeceres ◽  
Emilio Artacho

Use of ab initio molecular dynamics to predict the near-IR spectra of ices and application to astronomical models.


1993 ◽  
Vol 47 (9) ◽  
pp. 1324-1328 ◽  
Author(s):  
Curtis Marcott ◽  
A. E. Dowrey ◽  
Isao Noda

Dynamic two-dimensional infrared (2D IR) correlation maps are a convenient means of examining the information contained in time-resolved IR spectra. Dynamic 2D IR spectra can be collected with the use of either dispersive or Fourier transform (FT) IR spectrometers. Use of a step-scanning FT-IR spectrometer has advantages over conventional rapid-scan FT-IR spectrometry when one is acquiring time-resolved IR data on time scales faster than about 0.1 s, because the spectral multiplexing is removed from the time domain. Dynamic IR spectra of atactic polystyrene (undergoing a small-amplitude oscillatory strain) collected on both dispersive and FT instrumentation are compared. Although the dispersive approach produces higher signal-to-noise ratios over small spectral regions, the multiplex advantage makes the FT approach attractive when broader spectral coverages are required. The first vibrational circular dichroism (VCD) spectrum [of (–)- α;-pinene] collected on a step-scanning interferometer is also presented.


2006 ◽  
Vol 110 (17) ◽  
pp. 8531-8534 ◽  
Author(s):  
Yung Sam Kim ◽  
Robin M. Hochstrasser
Keyword(s):  
2D Ir ◽  

1985 ◽  
Vol 10 (3) ◽  
pp. 199-205 ◽  
Author(s):  
S. Calderone ◽  
G. Intilisano ◽  
P. Mantica ◽  
I. Montrosset ◽  
R. Orta

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