Literature DB >> 24588346

Blind prediction of binding affinities for charged supramolecular host-guest systems: achievements and shortcomings of DFT-D3.

Rebecca Sure1, Jens Antony, Stefan Grimme.   

Abstract

Association free energies ΔGa are calculated for two different types of host-guest systems, the rigid cucurbit[7]uril (CB7) and the basket shaped octa-acid (OA), and a number of charged guest molecules each by quantum chemical methods from first principles in the context of a recent blind test challenge (SAMPL4). For CB7, the overall agreement between theory and experiment is excellent. In comparison with all other submitted calculated relative ΔGa,rel values for this part of the blind test, our results ranked on top. Modeling the binding free energy in the case of the OA host mainly suffers from the problem that the binding situation is undefined with respect to the charge state and due to its intrinsic flexibility the host-guest complex is not represented well by a single configuration, but qualitative features of the binding process such as the proper binding orientation and the order of magnitude of ΔGa are represented in accord with the experimental expectations even though an accurate ranking is not possible.

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Year:  2014        PMID: 24588346     DOI: 10.1021/jp411616b

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  16 in total

1.  A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

Authors:  Jeffrey R Reimers; Dwi Panduwinata; Johan Visser; Yiing Chin; Chunguang Tang; Lars Goerigk; Michael J Ford; Maxine Sintic; Tze-Jing Sum; Michiel J J Coenen; Bas L M Hendriksen; Johannes A A W Elemans; Noel S Hush; Maxwell J Crossley
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-28       Impact factor: 11.205

2.  Evaluating dispersion forces for optimization of van der Waals complexes using a non-empirical functional.

Authors:  Alya A Arabi
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-11-13       Impact factor: 4.226

3.  Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Authors:  Juyong Lee; Florentina Tofoleanu; Frank C Pickard; Gerhard König; Jing Huang; Ana Damjanović; Minkyung Baek; Chaok Seok; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

4.  Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.

Authors:  Paulius Mikulskis; Daniela Cioloboc; Milica Andrejić; Sakshi Khare; Joakim Brorsson; Samuel Genheden; Ricardo A Mata; Pär Söderhjelm; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2014-04-04       Impact factor: 3.686

5.  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

6.  SAMPL6 host-guest challenge: binding free energies via a multistep approach.

Authors:  Yiğitcan Eken; Prajay Patel; Thomas Díaz; Michael R Jones; Angela K Wilson
Journal:  J Comput Aided Mol Des       Date:  2018-09-17       Impact factor: 3.686

7.  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

8.  SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics.

Authors:  Yiğitcan Eken; Nuno M S Almeida; Cong Wang; Angela K Wilson
Journal:  J Comput Aided Mol Des       Date:  2020-11-05       Impact factor: 3.686

9.  Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.

Authors:  Peng Xu; Tosaporn Sattasathuchana; Emilie Guidez; Simon P Webb; Kilinoelani Montgomery; Hussna Yasini; Iara F M Pedreira; Mark S Gordon
Journal:  J Chem Phys       Date:  2021-03-14       Impact factor: 3.488

10.  Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.

Authors:  Stefano Bosisio; Antonia S J S Mey; Julien Michel
Journal:  J Comput Aided Mol Des       Date:  2016-08-08       Impact factor: 3.686

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