Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.
Recently, two computational approaches that supply a density-functional-based quantum-chemical method with an empirical term accounting for London dispersion were introduced and found use in the studies of biomolecular systems, namely, DFT-D and SCC-DFTB-D. Here, we examine the performance and usability of these combined techniques for dealing with several tasks typically occurring in the research of biomolecules. The interaction energy of small biomolecular complexes agrees very well with the reference data yielded by correlated ab initio quantum chemical methods. In real-life studies aimed at interaction energy, structure, and infrared spectra, the mentioned methods provide results in good agreement with each other and with experiment (where available). The very favorable time demands of these approaches are discussed, and for each of them, a suitable area of use is proposed on the basis of the results of our analysis.
Kubar
Tomas
T
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences and Center of Biomolecules and Complex Molecular Systems, Flemingovo nAm. 2, 166 10 Praha 6, Czech Republic.
Jurecka
Petr
P
Cerný
Jirí
J
Rezac
Jan
J
Otyepka
Michal
M
Valdés
Haydée
H
Hobza
Pavel
P
D000596:Amino Acids / Q000737:chemistry*; D020029:Base Pairing; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004611:Ellipticines / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008954:Models, Biological; D008958:Models, Molecular; D015394:Molecular Structure; D009841:Oligonucleotides / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry*; D013059:Spectrum Analysis, Raman; D014732:Vibration
D000596:Amino Acids; D019941:Cyclin-Dependent Kinase Inhibitor p16; D004611:Ellipticines; D008024:Ligands; D009841:Oligonucleotides; D009842:Oligopeptides; C034192:ellipticine; D004247:DNA