Multiscale simulation on a light-harvesting molecular triad

The Journal of Physical Chemistry. B
Guoxiong SuMargaret S Cheung

Abstract

We have investigated the effect of solvation and confinement on an artificial photosynthetic material, carotenoid-porphyrin-C(60) molecular triad, by a multiscale approach and an enhanced sampling technique. We have developed a combined approach of quantum chemistry, statistical physics, and all-atomistic molecular dynamics simulation to determine the partial atomic charges of the ground-state triad. To fully explore the free energy landscape of triad, the replica exchange method was applied to enhance the sampling efficiency of the simulations. The confinement effects on the triad were modeled by imposing three sizes of spherocylindrical nanocapsules. The triad is structurally flexible under ambient conditions, and its conformation distribution is manipulated by the choice of water models and confinement. Two types of water models (SPC/E and TIP3P) are used for solvation. When solvated by SPC/E water, whose HOH angle follows an ideal tetrahedron, the structural characteristics of triad is compact in the bulk systems. However, under a certain nanosized confinement that drastically disrupts hydrogen bond networks in solvent, the triad favors an extended configuration. By contrast, the triad solvated by TIP3P water shows a set of...Continue Reading

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Apr 27, 1992·Physical Review Letters·A E García
Mar 27, 1999·Journal of Molecular Biology·M R Betancourt, D Thirumalai
Feb 15, 2001·Accounts of Chemical Research·D GustA L Moore
Sep 19, 2001·Biochemistry·H X Zhou, K A Dill
Oct 25, 2001·Journal of the American Chemical Society·H S Ashbaugh, M E Paulaitis
Oct 24, 2002·Journal of Computational Chemistry·Araz JakalianChristopher I Bayly
Jan 1, 1959·Advances in Protein Chemistry·W KAUZMANN
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
May 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Tanya M Raschke, Michael Levitt
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Oct 13, 2006·Journal of the American Chemical Society·S Vaitheeswaran, D Thirumalai
Oct 18, 2006·Proceedings of the National Academy of Sciences of the United States of America·Nathan S Lewis, Daniel G Nocera
Nov 10, 2006·The Journal of Chemical Physics·Tunna Baruah, Mark R Pederson
Jun 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Del LucentVijay S Pande
Jun 26, 2007·The Journal of Physical Chemistry. B·Margaret S Cheung, D Thirumalai
Sep 21, 2007·Journal of Computational Chemistry·M BasmaR J Woods
Oct 18, 2007·Nano Letters·Shao-Qing Zhang, Margaret S Cheung
Nov 13, 2007·Langmuir : the ACS Journal of Surfaces and Colloids·Palla Venkata Gopala RaoK G Ayappa
Apr 12, 2008·The Journal of Physical Chemistry. a·Alberto C RizziSilvia E Braslavsky
Apr 1, 2009·The Journal of Physical Chemistry. B·N SpallanzaniA Rubio
Sep 4, 2009·The Journal of Physical Chemistry. B·Dirar HomouzMargaret S Cheung
May 13, 2010·The Journal of Chemical Physics·Antonios SamiotakisMargaret S Cheung
Aug 11, 2011·PLoS Computational Biology·Qian WangMargaret S Cheung
Aug 23, 2011·Journal of the American Chemical Society·Jianhui Tian, Angel E Garcia
Apr 14, 2009·Journal of Chemical Theory and Computation·Tunna Baruah, Mark R Pederson
Jan 1, 2007·Journal of Chemical Theory and Computation·John D ChoderaKen A Dill

❮ Previous
Next ❯

Citations

Aug 18, 2017·Physical Chemistry Chemical Physics : PCCP·Oleg N StarovoytovMargaret S Cheung
Jul 10, 2021·The Journal of Chemical Physics·Dominikus BrianXiang Sun
Aug 12, 2015·The Journal of Physical Chemistry Letters·Arun K MannaBarry D Dunietz
Jun 10, 2014·The Journal of Physical Chemistry. B·Eudes Eterno Fileti, Vitaly V Chaban

❮ 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.