Two-colour sub-Doppler circular dichroism: a four-vector correlation molecular dynamics experiment for inelastic and reactive collisions

1991 ◽  
Vol 91 ◽  
pp. 91 ◽  
Author(s):  
Timothy L. D. Collins ◽  
Anthony J. McCaffery ◽  
Michael J. Wynn
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Vector Correlation ◽  
Reactive Collisions ◽  
Circular Dichroïsm

scholarly journals Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment

RSC Advances ◽  
2021 ◽  
Vol 11 (14) ◽  
pp. 8411-8419
Author(s):  
Jakub Kaminský ◽  
Valery Andrushchenko ◽  
Petr Bouř
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Nucleic Acids ◽  
Electronic Absorption ◽  
Magnetic Circular Dichroism ◽  
Circular Dichroism Spectra ◽  
Circular Dichroïsm ◽  
Magnetic Circular Dichroism Spectra

Electronic absorption, natural and magnetic circular dichroism spectra of several nucleosides are simulated to understand their dependence on molecular dynamics and environment, their sensitivity to nucleoside pairing and stacking in nucleic acids.

Calculation of the circular dichroism spectrum of cyclo(l-tyr-l-tyr) based on a molecular dynamics simulation

1994 ◽  
Vol 49 (2) ◽  
pp. 141-152 ◽  
Author(s):  
Jörg Fleischhauer ◽  
Joachim Grötzinger ◽  
Bernd Kramer ◽  
Peter Krüger ◽  
Axel Wollmer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulation ◽  
Circular Dichroism Spectrum ◽  
Dynamics Simulation ◽  
Circular Dichroïsm

scholarly journals PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures

2020 ◽  
Vol 48 (W1) ◽  
pp. W17-W24 ◽  
Author(s):  
Elliot D Drew ◽  
Robert W Janes
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Protein Structures ◽  
Experimental Spectrum ◽  
Md Simulations ◽  
Resonance Spectroscopy ◽  
Cd Spectra ◽  
Structure Information ◽  
Multiple Protein ◽  
Circular Dichroïsm

Abstract PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user. Using MD enables exploration of systems that cannot be monitored by direct experimentation. Validation of MD-derived data from these types of trajectories can be difficult via conventional structure-determining techniques such as crystallography or nuclear magnetic resonance spectroscopy. CD is an experimental technique that can provide protein structure information from such conditions. The website utilizes a much faster (minimum ∼1000×) and more accurate approach for calculating CD spectra than its predecessor, PDB2CD (1). As well as improving on the speed and accuracy of current methods, new analysis tools are provided to cluster predictions or compare them against experimental CD spectra. By identifying a subset of the closest predicted CD spectra derived from PDBMD2CD to an experimental spectrum, the associated cluster of structures could be representative of those found under the conditions in which the MD studies were undertaken, thereby offering an analytical insight into the results. PDBMD2CD is freely available at: https://pdbmd2cd.cryst.bbk.ac.uk.

scholarly journals Molecular Dynamics Ensemble Refinement of Intrinsically Disordered Peptides According to Deconvoluted Spectra from Circular Dichroism

2020 ◽  
Vol 118 (7) ◽  
pp. 1665-1678 ◽  
Author(s):  
Jacob C. Ezerski ◽  
Pengzhi Zhang ◽  
Nathaniel C. Jennings ◽  
M. Neal Waxham ◽  
Margaret S. Cheung
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Intrinsically Disordered ◽  
Disordered Peptides ◽  
Circular Dichroïsm
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