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Uracil-DNA Glycosylase Assay by Matrix-assisted Laser Desorption/Ionization Time-of-flight Mass Spectrometry Analysis
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Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case
Madhubani Mukherjee1, Divya Tripathi1, Martin Brehm2
1Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
Journal of Chemical Theory and Computation
|December 30, 2020
Summary
We developed a new quantum mechanics/molecular mechanics (QM/MM) protocol to accurately calculate electron affinity values for solvated nucleobases, showing excellent agreement with experimental data.
Area of Science:
- Computational Chemistry
- Quantum Chemistry
- Biophysical Chemistry
Background:
- Accurate calculation of electron affinity for nucleobases is crucial for understanding their chemical properties.
- Previous methods struggled with explicit solvation effects, leading to inaccuracies.
Purpose of the Study:
- To present a novel explicit solvation protocol for calculating electron affinity values of solvated nucleobases.
- To investigate the impact of solvation on electron affinity and assess the reliability of the new method.
Main Methods:
- Employed a quantum mechanics/molecular mechanics (QM/MM) approach.
- Utilized the domain-based pair natural orbital equation-of-motion coupled-cluster single-double (DPI-EOM-CCSD) method.
- Analyzed the sensitivity of electron affinity to solvation parameters like water molecule distribution and basis set size.
Main Results:
- Electron affinity values are sensitive to the local water distribution and convergence requires careful consideration of snapshots and water box size.
- Nonpolarizable water models overestimate electron affinity and introduce sensitivity to the QM region size.
- Calculated adiabatic electron affinity values show excellent agreement with experimental results.
Conclusions:
- The developed QM/MM protocol provides a controllable and accurate method for calculating electron affinity of solvated nucleobases.
- The study highlights the importance of explicit solvation and appropriate computational choices for reliable electron affinity predictions.
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