A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved?

2016 ◽  
Vol 18 (2) ◽  
pp. 866-877 ◽  
Author(s):  
Daniele Loco ◽  
Sandro Jurinovich ◽  
Lorenzo Di Bari ◽  
Benedetta Mennucci
Keyword(s):  
Circular Dichroism ◽  
Nucleic Acids ◽  
Cd Spectra ◽  
Electronic Circular Dichroism ◽  
Circular Dichroïsm

The CD spectra of nucleic acids can be simulated and interpreted through an excitonic approach combining TDDFT and polarizable MM.

Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum

2016 ◽  
Vol 22 (47) ◽  
pp. 17011-17019 ◽  
Author(s):  
Daniele Padula ◽  
Sandro Jurinovich ◽  
Lorenzo Di Bari ◽  
Benedetta Mennucci
Keyword(s):  
Circular Dichroism ◽  
Nucleic Acids ◽  
Electronic Circular Dichroism ◽  
Circular Dichroïsm

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 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.

scholarly journals Secondary structural characterization of the nucleic acids from circular dichroism spectra using extreme gradient boosting decision-tree algorithm

2020 ◽  
Author(s):  
Chakkarai Sathyaseelan ◽  
V Vinothini ◽  
Thenmalarchelvi Rathinavelan
Keyword(s):  
Circular Dichroism ◽  
Decision Tree ◽  
Nucleic Acids ◽  
Secondary Structures ◽  
Gradient Boosting ◽  
Decision Tree Algorithm ◽  
Cd Spectra ◽  
Tree Algorithm ◽  
Extreme Gradient Boosting ◽  
Circular Dichroïsm

AbstractNucleic acids exhibit a repertoire of conformational preference depending on the sequence and environment. Circular dichroism (CD) is an important and valuable tool for monitoring such secondary structural conformations of nucleic acids. Nonetheless, the CD spectral diversity associated with these structures poses a challenge in obtaining the quantitative information about the secondary structural content of a given CD spectrum. To this end, the competence of extreme gradient boosting decision-tree algorithm has been exploited here to predict the diverse secondary structures of nucleic acids. A curated library of 610 CD spectra corresponding to 16 different secondary structures of nucleic acids has been developed and used as a training dataset. For a test dataset of 242 CD spectra, the algorithm exhibited the prediction accuracy of 99%. For the sake of accessibility, the entire process is automated and implemented as a webserver, called CD-NuSS (CD to nucleic acids secondary structure) and is freely accessible at https://www.iith.ac.in/cdnuss/. The XGBoost algorithm presented here may also be extended to identify the hybrid nucleic acid topologies in future.

scholarly journals Mass-resolved electronic circular dichroism ion spectroscopy

Science ◽  
2020 ◽  
Vol 368 (6498) ◽  
pp. 1465-1468 ◽  
Author(s):  
Steven Daly ◽  
Frédéric Rosu ◽  
Valérie Gabelica
Keyword(s):  
Circular Dichroism ◽  
Three Dimensional ◽  
Polarized Light ◽  
Negative Ions ◽  
Data Interpretation ◽  
Electronic Circular Dichroism ◽  
Circularly Polarized Light ◽  
Chiral Compounds ◽  
Electron Photodetachment ◽  
Circular Dichroïsm

DNA and proteins are chiral: Their three-dimensional structures cannot be superimposed with their mirror images. Circular dichroism spectroscopy is widely used to characterize chiral compounds, but data interpretation is difficult in the case of mixtures. We recorded the electronic circular dichroism spectra of DNA helices separated in a mass spectrometer. We studied guanine-rich strands having various secondary structures, electrosprayed them as negative ions, irradiated them with an ultraviolet nanosecond optical parametric oscillator laser, and measured the difference in electron photodetachment efficiency between left and right circularly polarized light. The reconstructed circular dichroism ion spectra resembled those of their solution-phase counterparts, thereby allowing us to assign the DNA helical topology. The ability to measure circular dichroism directly on biomolecular ions expands the capabilities of mass spectrometry for structural analysis.

Chemical Constituents from Chloranthus elatior and Their Inhibitory Effect on Human Dihydroorotate Dehydrogenase

Planta Medica ◽  
2021 ◽  
Author(s):  
Qian Yang ◽  
An Jia ◽  
Xizi Liu ◽  
Shiyi Han ◽  
Siyang Fan
Keyword(s):  
Circular Dichroism ◽  
Chemical Constituents ◽  
Inhibitory Effect ◽  
Mass Spectrometric ◽  
Dihydroorotate Dehydrogenase ◽  
Active Compounds ◽  
Electronic Circular Dichroism ◽  
Aerial Parts ◽  
Ic50 Values ◽  
Circular Dichroïsm

AbstractA new sesquiterpene, chlorantholide G (1), a new sesquiterpene dimer, elatiolactone (2), and 2 new diterpenes, elatiorlabdane B (3) and elatiorlabdane C (4), together with 51 known compounds, were isolated from the aerial parts of Chloranthus elatior. The new structures including their absolute configurations were mainly established by mass spectrometric, NMR, and electronic circular dichroism experiments. All isolated compounds were tested for their anti-hDHODH activity. (4S,6R)-4-hydroxy-6-isopropyl-3-methylcyclohex-2-enone (5) and (4S,5R,9S,10R)-8(17),12,14-labdatrien-18-oic acid (29) were the most active compounds with IC50 values of 18.7 and 30.7 µM, respectively.

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