Conformational dependence of the circular dichroism spectra of single amino acids from plane-waves-based density functional theory calculations

The Journal of Physical Chemistry. B
E MolteniG Tiana

Abstract

We study the conformational dependence of circular dichroism (CD) spectra of amino acid molecules by means of an efficient ab initio DFT approach which is free from the typical gauge invariance issues arising with the use of localized basis sets and/or real-space grids. We analyze the dependence of the chiroptical spectra on the backbone dihedrals in the specific case of alanine and consider the role of side chain degrees of freedom at the examples of leucine, phenylalanine, and serine, whose side chains have different physicochemical properties. The results allow one to identify the most diagnostic regions of the CD spectra and to critically compare the conformations which match the experimental CD data with conformations extracted from the rotamer library. The inclusion of a solvation shell of explicit water molecules and its effect on the CD spectrum are analyzed at the example of alanine.

References

Jul 15, 1996·Physical Review. B, Condensed Matter·S GoedeckerJ Hutter
Jan 15, 1991·Physical Review. B, Condensed Matter·N Troullier, J L Martins
Oct 15, 1993·Physical Review. B, Condensed Matter· Del Sole R, R Girlanda
Aug 11, 2001·Physical Review Letters·S Ismail-BeigiS G Louie
Nov 13, 2003·Physical Review Letters·Chris J Pickard, Francesco Mauri
Jun 25, 2004·Analytical and Bioanalytical Chemistry·Márta KraszniBéla Noszál
Sep 16, 2004·Journal of the American Chemical Society·Susana BlancoJosé L Alonso
Mar 17, 2006·The Journal of Physical Chemistry. a·Matthew D Kundrat, Jochen Autschbach
Jun 9, 2006·Toxicology in Vitro : an International Journal Published in Association with BIBRA·Jillian G RouseNancy A Monteiro-Riviere
Jul 13, 2006·The Journal of Physical Chemistry. a·Anders OstedOve Christiansen
Jan 12, 2007·The Journal of Physical Chemistry. B·Branislav JansíkHans Agren
Mar 31, 2007·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·Prasad L Polavarapu
Apr 28, 2007·The Journal of Physical Chemistry. a·R MaulF Bechstedt
Sep 4, 2007·The Journal of Chemical Physics·Wojciech SkomorowskiTrygve Helgaker
Nov 8, 2007·The Journal of Physical Chemistry. a·T Daniel CrawfordMicah L Abrams
Mar 12, 2008·Journal of the American Chemical Society·Matthew D Kundrat, Jochen Autschbach
Mar 26, 2008·Chemical Society Reviews·Rein V Ulijn, Andrew M Smith
Jan 29, 2009·The Journal of Chemical Physics·Thomas Bondo PedersenKenneth Ruud
May 29, 2009·Physical Chemistry Chemical Physics : PCCP·Daniele VarsanoAngel Rubio
Sep 11, 2009·International Journal of Molecular Sciences·Jun-ichi TakahashiMasahiro Katoh
Sep 17, 2010·Angewandte Chemie·Uwe J MeierhenrichSøren V Hoffmann
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Apr 14, 2009·Journal of Chemical Theory and Computation·Matthew D Kundrat, Jochen Autschbach

❮ Previous
Next ❯

Citations

Jun 14, 2016·Journal of Chemical Theory and Computation·Nathaniel RaimbaultJ A Berger
Jan 10, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Daniele Padula, Gennaro Pescitelli
Jun 12, 2018·The Journal of Physical Chemistry. a·Jaime SilvaFernando Nogueira

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.