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

2013 ◽  
pp. 418-449
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Stochastic Simulation ◽  
Quasi Particle ◽  
2D Ir ◽  
Particle Approach

scholarly journals 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

2013 ◽  
Vol 139 (5) ◽  
pp. 054506 ◽  
Author(s):  
Myung Won Lee ◽  
Joshua K. Carr ◽  
Michael Göllner ◽  
Peter Hamm ◽  
Markus Meuwly
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Molecular Dynamics Simulations ◽  
2D Ir ◽  
Dynamics Simulations

scholarly journals Theoretical Investigations on the Reactivity of Methylidyne Radical toward 2,3,7,8-Tetrachlorodibenzo-p-Dioxin: A DFT and Molecular Dynamics Study

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2685 ◽  
Author(s):  
Weihua Wang ◽  
Wenling Feng ◽  
Wenliang Wang ◽  
Ping Li
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Hyperfine Coupling ◽  
Coupling Constants ◽  
Ab Initio Molecular Dynamics ◽  
Hyperfine Coupling Constants ◽  
Dynamics Simulations ◽  
Ch Radical

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.

scholarly journals Sensitivity of 2D IR Spectra to Peptide Helicity: A Concerted Experimental and Simulation Study of an Octapeptide

2009 ◽  
Vol 113 (35) ◽  
pp. 12037-12049 ◽  
Author(s):  
Neelanjana Sengupta ◽  
Hiroaki Maekawa ◽  
Wei Zhuang ◽  
Claudio Toniolo ◽  
Shaul Mukamel ◽  
...  
Keyword(s):  
Ir Spectra ◽  
Simulation Study ◽  
2D Ir ◽  
Peptide Helicity

scholarly journals Prediction of the near-IR spectra of ices by ab initio molecular dynamics

2019 ◽  
Vol 21 (18) ◽  
pp. 9433-9440 ◽  
Author(s):  
Rafael Escribano ◽  
Pedro C. Gómez ◽  
Belén Maté ◽  
Germán Molpeceres ◽  
Emilio Artacho
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Near Ir

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

Instrumental Aspects of Dynamic Two-Dimensional Infrared Spectroscopy

1993 ◽  
Vol 47 (9) ◽  
pp. 1324-1328 ◽  
Author(s):  
Curtis Marcott ◽  
A. E. Dowrey ◽  
Isao Noda
Keyword(s):  
Ir Spectra ◽  
Two Dimensional ◽  
Time Resolved ◽  
Ir Spectrometry ◽  
2D Ir ◽  
Scanning Interferometer ◽  
Atactic Polystyrene ◽  
Ft Ir ◽  
The Time Domain ◽  
Two Dimensional Infrared Spectroscopy

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.

scholarly journals Comparison of Linear and 2D IR Spectra in the Presence of Fast Exchange

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

Beam propagation in the ocean: Quasi-particle approach

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