Literature DB >> 25415491

Using dispersion-corrected density functional theory to understand supramolecular binding thermodynamics.

Jens Antony1, Rebecca Sure, Stefan Grimme.   

Abstract

A recently published theoretical approach employing a nondynamic structure model using dispersion-corrected density functional theory (DFT-D3) to calculate equilibrium free energies of association (Chem. Eur. J., 2012, 18, 9955-9964) is illustrated by its application to eight new supramolecular complexes. We compare with experimentally known binding constants which span the range from -3.3 to -20.3 kcal mol(-1). The mean deviation of calculated from measured ΔGa results in 0.4 kcal mol(-1), the mean absolute deviation in 1.8 kcal mol(-1) excluding two outliers for which the computed solvation free energies are identified as the largest error source. A survey of previous applications of the theoretical approach and related computational studies is given underlining its good accuracy. It is concluded that structures and gas phase interaction energies can be computed routinely with good to high accuracy (relative errors for interaction energies of 5-10%) for complexes with about 200-300 atoms.

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Year:  2015        PMID: 25415491     DOI: 10.1039/c4cc06722c

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN: 1359-7345            Impact factor:   6.222


  17 in total

1.  Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry.

Authors:  James Luccarelli; Robert S Paton
Journal:  J Org Chem       Date:  2019-01-09       Impact factor: 4.354

2.  Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods.

Authors:  Octav Caldararu; Martin A Olsson; Majda Misini Ignjatović; Meiting Wang; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2018-09-10       Impact factor: 3.686

3.  HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.

Authors:  Khaleel I Assaf; Mara Florea; Jens Antony; Niel M Henriksen; Jian Yin; Andreas Hansen; Zheng-Wang Qu; Rebecca Sure; Dieter Klapstein; Michael K Gilson; Stefan Grimme; Werner M Nau
Journal:  J Phys Chem B       Date:  2017-12-01       Impact factor: 2.991

4.  Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies.

Authors:  Jorge Escorihuela; Anita Das; Wilhelmus J E Looijen; Floris L van Delft; Adelia J A Aquino; Hans Lischka; Han Zuilhof
Journal:  J Org Chem       Date:  2017-12-20       Impact factor: 4.354

5.  Theoretical studies on a carbonaceous molecular bearing: association thermodynamics and dual-mode rolling dynamics.

Authors:  Hiroyuki Isobe; Kosuke Nakamura; Shunpei Hitosugi; Sota Sato; Hiroaki Tokoyama; Hideo Yamakado; Koichi Ohno; Hirohiko Kono
Journal:  Chem Sci       Date:  2015-02-18       Impact factor: 9.825

6.  Nanoscale π-π stacked molecules are bound by collective charge fluctuations.

Authors:  Jan Hermann; Dario Alfè; Alexandre Tkatchenko
Journal:  Nat Commun       Date:  2017-02-07       Impact factor: 14.919

7.  Interactions between large molecules pose a puzzle for reference quantum mechanical methods.

Authors:  Yasmine S Al-Hamdani; Péter R Nagy; Andrea Zen; Dennis Barton; Mihály Kállay; Jan Gerit Brandenburg; Alexandre Tkatchenko
Journal:  Nat Commun       Date:  2021-06-24       Impact factor: 14.919

Review 8.  Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.

Authors:  Nusret Duygu Yilmazer; Martin Korth
Journal:  Int J Mol Sci       Date:  2016-05-16       Impact factor: 5.923

9.  Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

Authors:  Majda Misini Ignjatović; Octav Caldararu; Geng Dong; Camila Muñoz-Gutierrez; Francisco Adasme-Carreño; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2016-08-26       Impact factor: 3.686

10.  Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).

Authors:  Octav Caldararu; Martin A Olsson; Christoph Riplinger; Frank Neese; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2016-09-06       Impact factor: 3.686

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