Interaction energy of DNA-base pairs and amino-acid pairs: DFT, DFTB and WFT calculations Tomáš Kubař , Petr Jurečka, Jirka Černý, Honza Řezáč, Michal Otyepka, Haydée Valdés and Pavel Hobza* Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague *[email protected]
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Interaction energyof DNAbase pairs and aminoacid pairs:
DFT, DFTB and WFT calculations
Tomáš Kubař, Petr Jurečka, Jirka Černý,Honza Řezáč, Michal Otyepka, Haydée Valdés
and Pavel Hobza*
Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences
● Correct prediction of the entire PES necessary,not only the interaction energy in minima
● Reason: minimization and dynamics● Example: minimization of the G–C stacked
complex using DFT (X3LYP/ccpVTZ)
● Error: no minimum on the PES for the stack – this complex is unstable and Hbonding prevails
Computational methods
● Modern QCh offers DFT– reliable except the treatment of dispersion energy – excellent timing (use of RI / density fitting)– needs adaptation to describe nonbonded interactions
1. Modification of the XC density functional2. Full DFT calculation with empirical correction for
dispersion energy (DFTD)3. Densityfunctional tightbinding with empirical
contribution of dispersion energy (SCCDFTBD)
DFTbased approaches – 1
● Modification of the XC density functional– blending of various functionals– eg. Zhao, Schultz, Truhlar
● J Chem Theor Comput 2, 364 (2006)– reliable interaction energy in the minima– the inclusion of exactexchange functional – decreased
speed– the exchange functional drives the complex formation
– incorrect distance dependence of energy for the dispersionbound complexes (r–1 or r–3 instead of r–6)
DFTbased approaches – 2
● Full DFT calculation with empirical correction to dispersion energy (DFTD)– eg. Grimme
● J Comp Chem, in press – r–6 function damped at middletoshort distances
r (nm)
E(kcal/mol)
DFTbased approaches – 2
● Full DFT calculation with empirical correction to dispersion energy (DFTD)– our implementation – Jurečka, Černý, Hobza, Salahub
● J Comp Chem, in press – r–6 function damped at middletoshort distances– no extra computational cost– RI approximation in DFT leads to favorable timing– (2) parameters – fitting on extensive CCSD(T) data
extrapolated to the CBS limit– testing on a large & balanced class of complexes– best performance – with TPSS / TZVP– facility to calculate normalmode frequencies
DFTbased approaches – 3
● Densityfunctional tightbinding– selfconsistent charges and empirical contribution of
dispersion energy– first introduction of empirical Edisp into a DFTlike
● J Chem Phys 114, 5149 (2001)– (surprisingly) good results– extremely fast compared to other approaches– for nonbonded complexes, no failure found yet– slightly inaccurate in the description of Hbonding
DNA – interaction of basesTesting
● Both Hbonded and stacked base pairs● Minimized geometry
AT W GC W mAmT H mGmC W AT S GC S mAmT S mGmC S40
30
20
10
0
10Interaction energy (kcal/mol)
B3LYP
● B3LYP– often used to describe biomolecular systems– strong Hbonded complexes; stacking – weak interaction
DNA – interaction of basesTesting
● Both Hbonded and stacked base pairs● Minimized geometry
AT W GC W mAmT H mGmC W AT S GC S mAmT S mGmC S40
30
20
10
0
10Interaction energy (kcal/mol)
B3LYP
CCSD(T)/CBS
● B3LYP incorrect for stacked complexes,there is strong attraction
DNA – interaction of basesTesting
● Both Hbonded and stacked base pairs● Minimized geometry
AT W GC W mAmT H mGmC W AT S GC S mAmT S mGmC S40
30
20
10
0
10Interaction energy (kcal/mol)
B3LYP
DFTDSCCDFTBD
CCSD(T)/CBS
● Generally perfect performance of D methods● Slightly weaker Hbonding by SCCDFTBD
DNA – interaction of basesApplication
● Analysis of 128 doublehelical DNA octamers● Interaction energy for 3 types of base pairs
– Hbonded, intra and interstrand stacked● Massive amount of calculation
– efficiency is crucial● Avg. total interaction energy per octamer:
● Idea of „relative importance“ of these interactions● Methods compare well