scholarly journals Relating circular dichroism to atomic structure by means of MD simulations and computed CD spectra with α-peptoids as an example

2020 ◽  
Vol 22 (23) ◽  
pp. 13192-13200
Author(s):  
Nicholus Bhattacharjee ◽  
Lionel Perrin ◽  
Franck Jolibois
Keyword(s):  
Circular Dichroism ◽  
Dft Calculations ◽  
Atomic Structure ◽  
3D Structure ◽  
Md Simulations ◽  
Cd Spectra ◽  
Electronic Circular Dichroism ◽  
Td Dft ◽  
Circular Dichroïsm

Accurate TD-DFT calculations of electronic circular dichroism have been performed to characterise the 3D structure of α-peptoids.

Vibronic structure in the far-UV electronic circular dichroism spectra of proteins

2015 ◽  
Vol 177 ◽  
pp. 329-344 ◽  
Author(s):  
Zhuo Li ◽  
David Robinson ◽  
Jonathan D. Hirst
Keyword(s):  
Circular Dichroism ◽  
Matrix Method ◽  
Vibrational Structure ◽  
Cd Spectra ◽  
Peptide Backbone ◽  
Electronic Circular Dichroism ◽  
Vibronic Structure ◽  
Far Ultraviolet ◽  
High Level ◽  
Circular Dichroïsm

The Franck–Condon effect is considered and the vibrational structure of the πnbπ* transition of the peptide backbone is incorporated into matrix method calculations of the electronic circular dichroism (CD) spectra of proteins in the far-ultraviolet. We employ the state-averaged CASPT2 method to calculate the ground and πnbπ* excited state geometries and frequencies of N-methylacetamide (NMA), which represents the peptide chromophore. The results of these calculations are used to incorporate vibronic levels of the excited states into the matrix method calculation. The CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of α-helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular β structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular β-sheet proteins. Our high-level ab initio calculations of the vibronic structure of the πnbπ* transition in NMA have provided some further insight into the physical origins of the nature of protein CD spectra in the far-UV.

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.

Tetraarylcyclobutadienecyclopentadienylcobalt Complexes: Synthesis, Electronic Spectra, Magnetic Circular Dichroism, Linear Dichroism, and TD DFT Calculations

2014 ◽  
Vol 33 (13) ◽  
pp. 3251-3264 ◽  
Author(s):  
Gregg S. Kottas ◽  
Thierry Brotin ◽  
Peter F. H. Schwab ◽  
Kamal Gala ◽  
Zdeněk Havlas ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Dft Calculations ◽  
Electronic Spectra ◽  
Magnetic Circular Dichroism ◽  
Linear Dichroism ◽  
Td Dft ◽  
Circular Dichroïsm

Magnetic circular dichroism spectroscopy and TD-DFT calculations of metal phthalocyanine anion and cation radical species

2006 ◽  
Vol 10 (10) ◽  
pp. 1219-1237 ◽  
Author(s):  
John Mack ◽  
Nagao Kobayashi ◽  
Martin J. Stillman
Keyword(s):  
Circular Dichroism ◽  
Dft Calculations ◽  
Magnetic Circular Dichroism ◽  
Cation Radical ◽  
Circular Dichroism Spectroscopy ◽  
Metal Phthalocyanine ◽  
Cation Radicals ◽  
Magnetic Circular Dichroism Spectroscopy ◽  
Td Dft ◽  
Circular Dichroïsm

The results of INDO/s and TD-DFT calculations for neutral ZnPc (−2), unligated [ ZnPc (−1)]+ and chloride anion ligated [( Cl ) ZnPc (−1)] cation radicals, the [ ZnPc (−3)]− radical anion and [ ZnPc (−4)]2− dianion species, performed on a set of B3LYP geometry optimizations are compared with magnetic circular dichroism spectral data. The two calculation methods predict spectra that are broadly similar. The TD-DFT calculations provide a significantly closer agreement with the experimental band centers in the UV region than was previously the case with INDO/s based calculations. The assignment of several key spectral features remains problematic, however, when band polarization information derived from magnetic circular dichroism spectroscopy is taken into consideration.

Electronic structures of azulene-fused porphyrins as seen by magnetic circular dichroism and TD-DFT calculations

2008 ◽  
Vol 102 (3) ◽  
pp. 466-471 ◽  
Author(s):  
Katsunori Nakai ◽  
Kei Kurotobi ◽  
Atsuhiro Osuka ◽  
Masanobu Uchiyama ◽  
Nagao Kobayashi
Keyword(s):  
Circular Dichroism ◽  
Dft Calculations ◽  
Electronic Structures ◽  
Magnetic Circular Dichroism ◽  
Td Dft ◽  
Circular Dichroïsm
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