On the calculation of magnetic properties of nucleic acids in liquid water with the sequential QM/MM method

15N NMR Shifts of Eumelanin Building Blocks in Water: A Combined Quantum Mechanics/Statistical Mechanics Approach

“…In comparison with the ASEC results, the presence of explicit water molecules that made hydrogen bonds gave a deshielding effect, with reductions for ( N1) of ppm and for ( N1) of ppm. For comparison, significant solvent shifts have also been reported for the magnetic shielding of protonated nitrogens of nucleic acids in liquid water due to the hydrogen bond effects [ 42 ]. Note that, in contrast with the gas phase results, similar magnetic shieldings of the protonated nitrogens indicated that an N NMR measurement could not distinguish the HQ and IQ monomers in water, whereas the ASEC one gave a difference of 2.22 ppm.…”

“…In the present work, we study the magnetic shielding constant ( N) of a selected set of eumelanin building blocks including monomers, dimers, and tetramers in aqueous solution using a sequential quantum mechanics/molecular mechanics (S-QM/MM) method [ 36 , 37 , 38 ] in combination with the average solvent electrostatic configuration (ASEC) model [ 39 ]. The structures of the liquid composed by the solute and solvent molecules in the thermodynamic equilibrium were generated using MM simulations whereas the QM calculations were performed using the density functional theory (DFT) that offer a good compromise between computational cost and accuracy for molecular magnetic properties in condensed phase [ 40 , 41 , 42 ]. Previous studies have been reported showing the importance of the analysis of electronic properties of building blocks for a better understanding of spectroscopic properties of eumelanin pigments [ 3 , 29 , 43 , 44 ].…”

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution

“…The charge point model for the solvent has been used and shows to be a good approximation to include the solvent effects on the quantum calculations performed. [29][30][31]44 The use of molecular dynamics allows the study to have a richer analysis, also contributing to estimate the conformational effects of (ILE) N structures on spectroscopic results. Our theoretical NMR results show good comparison with experimental results for oxygen atoms showing differences of only 2 ppm.…”

“…For the choice of this basis set functions and methodology, we have considered the number of the quantum mechanics calculations that should be performed during the work and, especially, the possibility of comparing the smallest structure (ILE) 1 results with the largest structure (ILE) 6 . 29,31,43,44,53 , especially for NMR spectroscopy which is strongly related to the electronic distribution of the structure 25,26 , as observed for neutral and charged polymers. Despite these modifications, the CHARMM36 description for the dipole moment is very similar to that observed in DFT calculations (treating the solvent as point charges).…”

“…NMR spectroscopy is a very powerful technique for determining fundamental characteristics of isolated molecules, such as neutral or charged polymers determining isomeric characteristics or even behavior in the distribution of atomic charges. 25,26 In solution, it characterize interactions between solutesolvent and have been applied in conjunction with Monte Carlo 27 or MD 28 simulation techniques for the inclusion of solvent effects on this nuclear property [29][30][31] . Allied to this technique, the absorption spectrum is able to determine electrical characteristics that are strongly influenced by solute-solvent interactions, especially for polar and protic solvents such as water 32,33 .…”