Reversible molecular switching of molecular beacon: controlling DNA hybridization kinetics and thermodynamics using mercury(ii) ions

2009 ◽  
pp. 322-324 ◽  
Author(s):  
Ronghua Yang ◽  
Jianyu Jin ◽  
Liping Long ◽  
Yongxiang Wang ◽  
Hao Wang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Molecular Beacon ◽  
Molecular Switching ◽  
Kinetics And Thermodynamics

scholarly journals Rapid DNA Hybridization Analysis Using a PDMS Microfluidic Sensor and a Molecular Beacon

2007 ◽  
Vol 23 (4) ◽  
pp. 401-405 ◽  
Author(s):  
Sungyong KIM ◽  
Lingxin CHEN ◽  
Sangyeop LEE ◽  
Gi Hun SEONG ◽  
Jaebum CHOO ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Molecular Beacon ◽  
Hybridization Analysis

Designing a Novel Molecular Beacon for Surface-Immobilized DNA Hybridization Studies

1999 ◽  
Vol 121 (12) ◽  
pp. 2921-2922 ◽  
Author(s):  
Xiaohong Fang ◽  
Xiaojing Liu ◽  
Sheldon Schuster ◽  
Weihong Tan
Keyword(s):  
Dna Hybridization ◽  
Molecular Beacon

scholarly journals Kinetics and thermodynamics of DNA hybridization on gold nanoparticles

2009 ◽  
Vol 37 (11) ◽  
pp. 3756-3765 ◽  
Author(s):  
Chunlai Chen ◽  
Wenjuan Wang ◽  
Jing Ge ◽  
Xin Sheng Zhao
Keyword(s):  
Gold Nanoparticles ◽  
Dna Hybridization ◽  
Kinetics And Thermodynamics

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

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