Assessment of the MP2 Method, along with Several Basis Sets, for the Computation of Interaction Energies of Biologically Relevant Hydrogen Bonded and Dispersion Bound Complexes

2007 ◽  
Vol 111 (33) ◽  
pp. 8257-8263 ◽  
Author(s):  
Kevin E. Riley ◽  
Pavel Hobza
Keyword(s):  
Basis Sets ◽  
Interaction Energies ◽  
Biologically Relevant ◽  
Mp2 Method ◽  
Hydrogen Bonded

The assessment of density functionals for DNA–protein stacked and T-shaped complexes

2010 ◽  
Vol 88 (8) ◽  
pp. 815-830 ◽  
Author(s):  
Lesley R. Rutledge ◽  
Stacey D. Wetmore
Keyword(s):  
Amino Acid ◽  
Potential Energy ◽  
Large Scale ◽  
Enzymatic Reaction ◽  
Basis Sets ◽  
Density Functionals ◽  
Interaction Energies ◽  
Π Interactions ◽  
Hybrid Techniques ◽  
Semi Empirical

The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.

Universal Gaussian basis functions in relativistic quantum chemistry: atomic Dirac–Fock–Coulomb and Dirac–Fock–Breit calculations

1992 ◽  
Vol 70 (6) ◽  
pp. 1822-1826 ◽  
Author(s):  
G. L. Malli ◽  
A. B. F. Da Silva ◽  
Yasuyuki Ishikawa
Keyword(s):  
Relativistic Quantum ◽  
Basis Set ◽  
Basis Sets ◽  
Interaction Energies ◽  
Gaussian Basis Sets ◽  
Consistent Field ◽  
Self Consistent ◽  
Self Consistent Field ◽  
Gaussian Basis Set ◽  
Good Agreement

Matrix Dirac–Fock–Coulomb and Dirac–Fock–Breit self-consistent field calculations are performed for a number of neutral atoms. He (Z = 2) through Xe (Z = 54), using the universal Gaussian basis set (18s, 12p, 11d) reported recently by Da Silva etal. The total Dirac–Fock–Coulomb, the Dirac–Fock–Breit, and the Breit interaction energies calculated with this universal Gaussian basis set are in good agreement with the corresponding values obtained by using an extensive well-tempered Gaussian basis set for the He through Ca (Z = 20) atoms. Although this universal Gaussian basis set is inadequate for the calculation of total Dirac–Fock–Coulomb and Dirac–Fock–Breit energies for the Kr, Sr, and Xe atoms, the Breit interaction energies calculated with this basis for these three atoms are in very good agreement with the corresponding Breit interaction energies obtained by using the extensive well-tempered Gaussian basis sets. Work is in progress to generate a more extensive and energetically better universal Gaussian basis set for He through Xe for its use in non-relativistic Hartree–Fock as well as Dirac–Fock self-consistent field calculations on polyatomics involving heavy atoms.

Ab initio study of van der Waals and hydrogen-bonded molecular crystals with a periodic local-MP2 method

CrystEngComm ◽  
2010 ◽  
Vol 12 (8) ◽  
pp. 2429 ◽  
Author(s):  
Lorenzo Maschio ◽  
Denis Usvyat ◽  
Bartolomeo Civalleri
Keyword(s):  
Ab Initio ◽  
Van Der Waals ◽  
Molecular Crystals ◽  
Ab Initio Study ◽  
Mp2 Method ◽  
Hydrogen Bonded

Interaction energies between metal ions (Zn2+ and Cd2+ ) and biologically relevant ligands

2013 ◽  
Vol 113 (23) ◽  
pp. 2554-2562 ◽  
Author(s):  
Emma Ahlstrand ◽  
Daniel Spångberg ◽  
Kersti Hermansson ◽  
Ran Friedman
Keyword(s):  
Metal Ions ◽  
Interaction Energies ◽  
Biologically Relevant

Rapid evaluation of the interaction energies for carbohydrate-containing hydrogen-bonded complexes via the polarizable dipole–dipole interaction model combined with NBO or AM1 charge

RSC Advances ◽  
2015 ◽  
Vol 5 (9) ◽  
pp. 6452-6461 ◽  
Author(s):  
Jiao-Jiao Hao ◽  
Chang-Sheng Wang
Keyword(s):  
Hydrogen Bond ◽  
Interaction Model ◽  
Dipole Interaction ◽  
Rapid Evaluation ◽  
Interaction Energies ◽  
Bonded Complexes ◽  
Hydrogen Bonded

The polarizable dipole–dipole interaction model has been developed to rapidly and accurately estimate the hydrogen bond distances and interaction energies for carbohydrate-containing hydrogen-bonded complexes.

Accurate evaluation of SCF and MP2 components of interaction energies. Complexes of HF, OH2, and NH3 with Li+

1988 ◽  
Vol 53 (10) ◽  
pp. 2214-2229 ◽  
Author(s):  
Małgorzata M. Szczęśniak ◽  
Steve Scheiner
Keyword(s):  
Point Charge ◽  
Basis Set ◽  
Basis Sets ◽  
Interaction Energies ◽  
Multipole Moments ◽  
Gaussian Basis Sets ◽  
Basis Set Superposition Error ◽  
Polarization Functions ◽  
Selection Of ◽  
Correlation Corrections

High-quality Gaussian basis sets of the well-tempered type, containing three sets of polarization functions on all atoms, are used to investigate the interaction of Li+ with HF, OH2, and NH3. These sets reproduce the SCF and MP2 energies of the various monomers very well and, moreover, accurately treat the multipole moments and polarizabilities of the monomers. When applied to the complexes, the sets are essentially free of primary and secondary basis set superposition error at the SCF level; MP2 extension effects are also completely negligible while basis set superposition effects are small but non-negligible. Analysis of the correlation corrections to the molecular properties, coupled with comparison of the interaction of the bases with a point charge, provides a straightforward explanation of correlation contributions to the interaction energy. Recommendations are provided to guide selection of basis sets for molecular interactions so as to avoid distortion of the various components.

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