scholarly journals Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

2018 ◽  
Vol 9 (41) ◽  
pp. 7902-7911 ◽  
Author(s):  
Antonio Francés-Monerris ◽  
Hugo Gattuso ◽  
Daniel Roca-Sanjuán ◽  
Iñaki Tuñón ◽  
Marco Marazzi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Hydrogen Transfer ◽  
Proton Transfers ◽  
Out Of Plane ◽  
Dynamics Simulations

Multiscale molecular dynamics simulations reveal out-of-plane distortions that favour DNA photostability. A novel photostability mechanism involving four proton transfers and triggered by a nearby Na+ ion is also unveiled.

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations

2021 ◽  
Vol 23 (14) ◽  
pp. 8525-8540
Author(s):  
Mudong Feng ◽  
Michael K. Gilson
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Molecular Motors ◽  
Motor Performance ◽  
Molecular Simulations ◽  
Mechanistic Analysis ◽  
Dynamics Simulations ◽  
Shed Light

Ground-state and excited-state molecular dynamics simulations shed light on the rotation mechanism of small, light-driven molecular motors and predict motor performance. How fast can they rotate; how much torque and power can they generate?

Ab Initio Molecular Dynamics Simulations of an Excited State of X-(H2O)3(X = Cl, I) Complex

2005 ◽  
Vol 109 (42) ◽  
pp. 9419-9423 ◽  
Author(s):  
M. Kołaski ◽  
Han Myoung Lee ◽  
Chaeho Pak ◽  
M. Dupuis ◽  
Kwang S. Kim
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

2016 ◽  
Vol 195 ◽  
pp. 237-251 ◽  
Author(s):  
Rafał Szabla ◽  
Robert W. Góra ◽  
Mikołaj Janicki ◽  
Jiří Šponer
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Energy Surface ◽  
Water Molecules ◽  
Dynamics Simulations

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.

scholarly journals Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite

2020 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Soil Mineral ◽  
P Efficiency ◽  
Proton Transfers ◽  
Dynamics Simulations ◽  
Near Future ◽  
Level Analysis ◽  
Phosphate Groups

Today's fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future and hence, effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to become unavailable to plants. Understanding P interaction with these minerals would help efforts that improve P efficiency. To this end we performed a molecular level analysis of the interaction of common organic P compounds (glycerolphosphate [GP] & inositol hexaphosphate [IHP]) with the abundant soil mineral (goethite) in presence of water. Molecular dynamics simulations are performed for goethite-IHP/GP-water complexes using the multiscale quantum mechanics/molecular mechanics method. Results show that GP forms monodentate (M) and bidentate mononuclear (B) motifs with B being more stable than M. IHP interacts through multiple phosphate groups with the \textbf{3M} motif being most stable. The order of goethite-IHP/GP interaction energies is: GP M < GP B < IHP M < IHP 3M. Water is important in these interactions as multiple proton transfers occur and hydrogen bonds are formed between goethite--IHP/GP complexes and water. We also present theoretically calculated infrared spectra which match reasonably well with frequencies reported in literature.

NEXMD Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations

2020 ◽  
Vol 16 (9) ◽  
pp. 5771-5783 ◽  
Author(s):  
Walter Malone ◽  
Benjamin Nebgen ◽  
Alexander White ◽  
Yu Zhang ◽  
Huajing Song ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Software Package ◽  
Dynamics Simulations
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