scholarly journals Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations

2013 ◽  
Vol 15 (29) ◽  
pp. 12322 ◽  
Author(s):  
Akira Nakayama ◽  
Yu Harabuchi ◽  
Shohei Yamazaki ◽  
Tetsuya Taketsugu
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Calculations ◽  
Nonradiative Decay ◽  
Potential Energy Calculations ◽  
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.

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

Melting at Mg/Al interface in Mg-Al-Mg nanolayer by molecular dynamics simulations

2021 ◽  
Author(s):  
Xue-Qi Lv ◽  
Xiong-Ying Li
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Distribution Function ◽  
Potential Energy ◽  
Density Distribution ◽  
Molecular Dynamics Simulations ◽  
Regional Research ◽  
Melting Temperatures ◽  
Essential Step ◽  
Dynamics Simulations

Abstract The melting at the magnesium/aluminum (Mg/Al) interface is an essential step during the fabrications of Mg-Al structural materials and biomaterials. We carried out molecular dynamics simulations on the melting at the Mg/Al interface in a Mg-Al-Mg nanolayer via analyzing the changes of average atomic potential energy, Lindemann index, heat capacity, atomic density distribution and radial distribution function with temperature. The melting temperatures (T m) of the nanolayer and the slabs near the interface are significantly sensitive to the heating rate (v h) over the range of v h≤4.0 K/ps. The distance (d) range in which the interface affects the melting of the slabs is predicted to be (-98.2, 89.9) Å at v h→0, if the interface is put at d=0 and Mg (Al) is located at the left (right) side of the interface. The (T m) of the Mg (Al) slab just near the interface (e.g., d=4.0 Å) is predicted to be 926.8 K (926.6 K) at v h→0, with 36.9 K (37.1 K) below 963.7 K for the nanolayer. These results highlight the importance of regional research on the melting at an interface in the nanolayers consisting of two different metals.

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