Literature DB >> 26627172

Density Functionals for Noncovalent Interaction Energies of Biological Importance.

Yan Zhao1, Donald G Truhlar1.   

Abstract

Forty density functionals and one wavefunction method are assessed against a recently published database of accurate noncovalent interaction energies of biological importance. The comparison shows that two newly developed density functional theory (DFT) methods, PWB6K and M05-2X, give the best performance for this benchmark database of 22 noncovalent complexes, including both hydrogen-bonding and dispersion-dominated complexes. In contrast, the more popular B3LYP and PBEh functionals fail to describe the interactions in the dispersion-dominated complexes. The local spin density approximation and BHandH functionals give good performance for dispersion-dominated interactions at the expense of a large error for hydrogen bonding. PWB6K and M05-2X constitute a new generation of DFT methods based on simultaneously optimized exchange and correlation functionals that include kinetic energy density in both the exchange and correlation functional, and the present study confirms that they have greatly improved performance for noncovalent interactions as compared to previous DFT methods. We interpret this as being due to an improved treatment of medium-range correlation effects by the exchange-correlation functional. We recommend the PWB6K and M05-2X methods for investigating large biological systems and soft materials.

Entities:  

Year:  2007        PMID: 26627172     DOI: 10.1021/ct6002719

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  35 in total

1.  New organic FET-like photoactive device, experiments and DFT modeling.

Authors:  I Kratochvilová; S Nesprek; J Sebera; S Zális; M Pavelka; G Wang; J Sworakowski
Journal:  Eur Phys J E Soft Matter       Date:  2008-04-09       Impact factor: 1.890

2.  Insight into the reaction mechanism of cis,cis-muconate lactonizing enzymes: a DFT QM/MM study.

Authors:  Tuanjai Somboon; Matthew Paul Gleeson; Supa Hannongbua
Journal:  J Mol Model       Date:  2011-05-04       Impact factor: 1.810

Review 3.  Quantum mechanical investigations of organocatalysis: mechanisms, reactivities, and selectivities.

Authors:  Paul Ha-Yeon Cheong; Claude Y Legault; Joann M Um; Nihan Çelebi-Ölçüm; K N Houk
Journal:  Chem Rev       Date:  2011-06-28       Impact factor: 60.622

4.  Density functional theory studies of the extent of hole delocalization in one-electron oxidized adenine and guanine base stacks.

Authors:  Anil Kumar; Michael D Sevilla
Journal:  J Phys Chem B       Date:  2011-03-21       Impact factor: 2.991

5.  A systematical comparison of DFT methods in reproducing the interaction energies of halide series with protein moieties.

Authors:  Xiuhong Liu; Peng Zhou; Zhicai Shang
Journal:  J Mol Model       Date:  2011-09-09       Impact factor: 1.810

6.  How Does Mg2+ Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair.

Authors:  Antarip Halder; Rohit Roy; Dhananjay Bhattacharyya; Abhijit Mitra
Journal:  Biophys J       Date:  2017-05-12       Impact factor: 4.033

7.  Electronic structure theory based study of proline interacting with gold nano clusters.

Authors:  Sandhya Rai; Harjinder Singh
Journal:  J Mol Model       Date:  2012-12-21       Impact factor: 1.810

8.  The accuracy of quantum chemical methods for large noncovalent complexes.

Authors:  Robert Sedlak; Tomasz Janowski; Michal Pitoňák; Jan Rezáč; Peter Pulay; Pavel Hobza
Journal:  J Chem Theory Comput       Date:  2013-08-13       Impact factor: 6.006

9.  Insights into the strength and nature of carbene···halogen bond interactions: a theoretical perspective.

Authors:  Mehdi D Esrafili; Nafiseh Mohammadirad
Journal:  J Mol Model       Date:  2013-03-02       Impact factor: 1.810

10.  A theoretical investigation of the characteristics of hydrogen/halogen bonding interactions in dibromo-nitroaniline.

Authors:  Mehdi D Esrafili
Journal:  J Mol Model       Date:  2012-12-08       Impact factor: 1.810

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