Spin-state dependence of the structural and vibrational properties of solvated iron(ii) polypyridyl complexes from AIMD simulations: aqueous [Fe(bpy)3]Cl2, a case study

2018 ◽  
Vol 20 (9) ◽  
pp. 6236-6253 ◽  
Author(s):  
Latévi M. Lawson Daku
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Ir Spectrum ◽  
State Of The Art ◽  
State Dependence ◽  
Vibrational Properties ◽  
Polypyridyl Complexes ◽  
Dynamics Simulations

LS and HS IR spectra of aqueous [Fe(bpy)3]2+ and corresponding HS–LS difference IR spectrum as obtained from state-of-the-art ab initio molecular dynamics simulations applied to the determination of the structural and vibrational properties of the solvated complex.

scholarly journals Theoretical Investigations on the Reactivity of Methylidyne Radical toward 2,3,7,8-Tetrachlorodibenzo-p-Dioxin: A DFT and Molecular Dynamics Study

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2685 ◽  
Author(s):  
Weihua Wang ◽  
Wenling Feng ◽  
Wenliang Wang ◽  
Ping Li
Keyword(s):  
Molecular Dynamics ◽  
Ir Spectra ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Hyperfine Coupling ◽  
Coupling Constants ◽  
Ab Initio Molecular Dynamics ◽  
Hyperfine Coupling Constants ◽  
Dynamics Simulations ◽  
Ch Radical

To explore the potential reactivity of the methylidyne radical (CH) toward 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the reaction mechanism between them has been systematically investigated employing the density functional theory (DFT) and ab initio molecular dynamics simulations. The relevant thermodynamic and kinetic parameters in the possible reaction pathways have been discussed as well as the IR spectra and hyperfine coupling constants (hfcc’s) of the major products. Different from the reaction of the CH radical with 2,3,7,8-tetrachlorodibenzofuran, CH radical can attack all the C-C bonds of TCDD to form an initial intermediate barrierlessly via the cycloaddition mechanism. After then, the introduced C-H bond can be further inserted into the C-C bond of TCDD, resulting in the formation of a seven-membered ring structure. The whole reactions are favorable thermodynamically and kinetically. Moreover, the major products have been verified by ab initio molecular dynamics simulations. The distinct IR spectra and hyperfine coupling constants of the major products can provide some help for their experimental detection and identification. In addition, the reactivity of the CH radical toward the F- and Br-substituted TCDDs has also been investigated. Hopefully, the present findings can provide new insights into the reactivity of the CH radical in the transformation of TCDD-like dioxins.

scholarly journals Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

2019 ◽  
Vol 21 (1) ◽  
pp. 1-31 ◽  
Author(s):  
Lindong Weng ◽  
Shannon L. Stott ◽  
Mehmet Toner
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Motion ◽  
State Of The Art ◽  
Level Structure ◽  
Cost Effective ◽  
Atomic Level ◽  
Computational Research ◽  
Dynamics Simulations ◽  
Biological Entities

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

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