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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and
Haydee Valdes1, Kristýna Pluhácková, Michal Pitonák
1Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic. haydee.valdes@marge.uochb.cas.cz
Physical Chemistry Chemical Physics : PCCP
|May 10, 2008
Summary
Accurate peptide studies require methods accounting for London dispersion forces. M06-2X and TPSS-D functionals best capture these interactions, outperforming others like B3LYP.
Area of Science:
- Computational Chemistry
- Quantum Chemistry
- Biophysics
Background:
- Intramolecular interactions in small peptides are dominated by dispersion forces.
- Accurate theoretical studies necessitate methods that properly account for London dispersion.
- Aromatic residues like phenylalanine (F) and tryptophan (W) significantly influence peptide interactions.
Purpose of the Study:
- To evaluate various computational methods for studying peptides containing aromatic residues.
- To identify the most accurate and efficient methods for calculating peptide energies and geometries.
- To compare wavefunction theory and density functional theory (DFT) approaches, including dispersion-corrected methods.
Main Methods:
- Quantum chemical calculations were performed on five peptides: WG, WGG, FGG, GGF, and GFA.
- Assessed methods include MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D, and ff99 force field.
- Benchmark data was obtained using CCSD(T)/complete basis set (CBS) limit calculations.
Main Results:
- The ff99 force field is not recommended due to issues with atomic charge assignment.
- Tight-binding DFT-D provides efficient and reliable geometries, suitable for screening.
- M06-2X and TPSS-D functionals demonstrated the best performance among DFT methods by incorporating dispersion energy.
- Wavefunction theory methods yielded results comparable to the CCSD(T)/CBS benchmark for energies and geometries.
- Standard DFT functionals like B3LYP and TPSS, without dispersion correction, showed systematic failures.
Conclusions:
- Methods incorporating London dispersion forces, such as M06-2X and TPSS-D, are crucial for accurate peptide studies.
- Tight-binding DFT-D is a valuable tool for preliminary geometric analysis.
- Wavefunction theory methods provide high accuracy but are computationally more demanding.
- The choice of computational method significantly impacts the reliability of results in peptide research.
