27 research outputs found
Reduction Potential Predictions for Some 3-Aryl-Quinoxaline-2-Carbonitrile 1,4-Di-N-Oxide Derivatives with Known Anti-Tumor Properties
The ability for DFT: B3LYP calculations using the 6-31g and lanl2dz basis sets to predict the electrochemical properties of twenty (20) 3-aryl-quinoxaline-2-carbonitrile 1,4-di-N-oxide derivatives with varying degrees of cytotoxic activity in dimethylformamide (DMF) was investigated. There was a strong correlation for the first reduction and moderate-to-low correlation of the second reduction of the diazine ring between the computational and the experimental data, with the exception of the derivative containing the nitro functionality. The four (4) nitro group derivatives are clear outliers in the overall data sets and the derivative E4 is ill-behaved. The remaining three (3) derivatives containing the nitro groups had a strong correlation between the computational and experimental data; however, the computational data falls substantially outside of the expected range
MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the <i>Oxytricha nova</i> G‑Quadruplex
A generalization of the Moving-Domain
Quantum Mechanics/Molecular
Mechanics (MoD-QM/MM) hybrid method [Gascon, J. A.; Leung, S. S. F.;
Batista, E. R.; Batista, V. S. <i>J. Chem. Theory Comput.</i> <b>2006</b>, <i>2</i>, 175–186] is introduced
to provide a self-consistent computational protocol for structural
refinement of extended systems. The method partitions the system into
molecular domains that are iteratively optimized as quantum mechanical
(QM) layers embedded in their surrounding molecular environment to
obtain an ab initio quality description of the geometry and the molecular
electrostatic potential of the extended system composed of those constituent
fragments. The resulting methodology is benchmarked as applied to
model systems that allow for full QM optimization as well as through
refinement of the hydrogen bonding geometry in <i>Oxytricha nova</i> guanine quadruplex for which several studies have been reported,
including the X-ray structure and NMR data. Calculations of <sup>1</sup>H NMR chemical shifts based on the gauge independent atomic orbital
(GIAO) method and direct comparisons with experiments show that solvated
MoD-QM/MM structures, sampled from explicit solvent molecular dynamics
simulations, allow for NMR simulations in much improved agreement
with experimental data than models based on the X-ray structure or
those optimized using classical molecular mechanics force fields