Scholarship 23/14766-7 - Propriedades magnéticas, Ressonância magnética nuclear - BV FAPESP
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Study of Canonical and Artificial Metal-mediated Base Pairs in Solution by ab initio Molecular Dynamics and Relativistic NMR Calculations

Grant number: 23/14766-7
Support Opportunities:Scholarships in Brazil - Doctorate
Start date until: March 01, 2024
End date until: July 31, 2027
Field of knowledge:Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
Principal Investigator:Lucas Colucci Ducati
Grantee:Lucas Pinheiro Coutinho
Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

Metal-mediated base pairs (MMbp) are canonical and artificial nitrogenous bases that can pair with identical nucleobases or form non-natural pairs through metalation with transition metals in solution. The applications of MMbps range from the development of heavy metal sensors, biological logic gate devices for cell signaling and the construction of molecular machines through the manipulation of alternative base pairs. The most studied PBmms are those with Hg(II) and Ag(I) complexed with DNA duplex systems of T-Hg-T and C-Ag-C. The nuclear magnetic resonance (NMR) technique is of great assistance in elucidating the structure and synthesis of PBmms, using the magnetic properties such as chemical shift (5ÿ), shielding tensor (5) and indirect spin-spin coupling constant (5=) as analysis parameters mainly for 107,109Ag(I) e 199Hg(II) NMR. However, although studies in the literature use relativistic corrections in DFT (Density Functional Theory) calculations with the ZORA (Zero Order Regular Approximation), the dynamic effect of the explicit solvent is not analyzed, implying variations in the obtained results. Therefore, in the proposed study, is intend to investigate the effect of the explicit solvent on canonical and artificial MMbp systems, mainly with Ag and Hg, carrying out a study on the dynamic effect of the coordination of water molecules and conformational changes through the combination of theoretical DFT calculations with molecular dynamics using the Ab initio molecular dynamics (AIMD) method.

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