Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

2006 ◽  
Vol 8 (17) ◽  
pp. 1985-1993 ◽  
Author(s):  
Petr Jurečka ◽  
Jiří Šponer ◽  
Jiří Černý ◽  
Pavel Hobza
Keyword(s):  
Basis Set ◽  
Interaction Energies ◽  
Base Pairs ◽  
Model Complexes ◽  
Dna Base ◽  
Benchmark Database ◽  
Dna Base Pairs ◽  
Complete Basis Set ◽  
Complete Basis Set Limit ◽  
Small Model

scholarly journals Importance of Model Size in Quantum Mechanical Studies of DNA Intercalation

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Binding Site ◽  
Small Molecule ◽  
Computational Cost ◽  
Dna Intercalation ◽  
Interaction Energies ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Model Size ◽  
Reliable Interaction

There is currently a dearth of effective computational tools to design nucleobase-targeting small molecules and molecular mechanics force-fields for nucleobases lag behind their protein-focused counterparts. While quantum chemical methods can provide reliable interaction energies for small molecule-nucleobase interactions, these come at a steep computational cost. As a first step toward refining available tools for predicting small molecule-nucleobase interactions, we assessed the convergence of DFT-computed interaction energies with increasing binding site model size. We find that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in non-covalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.<br>

scholarly journals DFT Description of Intermolecular Forces between 9-Aminoacridines and DNA Base Pairs

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Sandra Cotes Oyaga ◽  
José Cotuá Valdés ◽  
Sigrid Borja Paez ◽  
Keylin Hurtado Marquez
Keyword(s):  
Dipole Moments ◽  
Intermolecular Forces ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Base Pairs ◽  
Charge Delocalization ◽  
Drug Diffusion ◽  
Dna Base ◽  
B3lyp Method ◽  
Dna Base Pairs

The B3LYP method with 6-31G* basis set was used to predict the geometries of five 9-aminoacridines (9-AA 1(a–e)), DNA base pairs, and respective complexes. Polarizabilities, charge distribution, frontier molecular orbital (FMO), and dipole moments were used to analyze the nature of interactions that allow reasonable drug diffusion levels. The results showed that charge delocalization, high polarizabilities, and high dipole moments play an important role in intermolecular interactions with DNA. The interactions of 9-AA 1(a–e) with GC are the strongest. 9-AA 1(d) displayed the strongest interaction and 9-AA 1(b) the weakest.

scholarly journals Importance of Model Size in Quantum Mechanical Studies of DNA Intercalation

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Binding Site ◽  
Small Molecule ◽  
Computational Cost ◽  
Dna Intercalation ◽  
Interaction Energies ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Model Size ◽  
Reliable Interaction

There is currently a dearth of effective computational tools to design nucleobase-targeting small molecules and molecular mechanics force-fields for nucleobases lag behind their protein-focused counterparts. While quantum chemical methods can provide reliable interaction energies for small molecule-nucleobase interactions, these come at a steep computational cost. As a first step toward refining available tools for predicting small molecule-nucleobase interactions, we assessed the convergence of DFT-computed interaction energies with increasing binding site model size. We find that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in non-covalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.<br>

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