Literature DB >> 25747054

Communication: Accurate hydration free energies at a wide range of temperatures from 3D-RISM.

Maksim Misin1, Maxim V Fedorov1, David S Palmer2.   

Abstract

We present a new model for computing hydration free energies by 3D reference interaction site model (3D-RISM) that uses an appropriate initial state of the system (as suggested by Sergiievskyi et al.). The new adjustment to 3D-RISM theory significantly improves hydration free energy predictions for various classes of organic molecules at both ambient and non-ambient temperatures. An extensive benchmarking against experimental data shows that the accuracy of the model is comparable to (much more computationally expensive) molecular dynamics simulations. The calculations can be readily performed with a standard 3D-RISM algorithm. In our work, we used an open source package AmberTools; a script to automate the whole procedure is available on the web (https://github.com/MTS-Strathclyde/ISc).

Entities:  

Year:  2015        PMID: 25747054     DOI: 10.1063/1.4914315

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

1.  SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling.

Authors:  Tyler Luchko; Nikolay Blinov; Garrett C Limon; Kevin P Joyce; Andriy Kovalenko
Journal:  J Comput Aided Mol Des       Date:  2016-09-01       Impact factor: 3.686

Review 2.  Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions.

Authors:  Masahiro Kinoshita; Tomohiko Hayashi
Journal:  Biophys Rev       Date:  2020-03-17

3.  Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent.

Authors:  Dipankar Roy; Andriy Kovalenko
Journal:  J Comput Aided Mol Des       Date:  2019-10-21       Impact factor: 3.686

4.  Small molecule hydration energy and entropy from 3D-RISM.

Authors:  J Johnson; D A Case; T Yamazaki; S Gusarov; A Kovalenko; T Luchko
Journal:  J Phys Condens Matter       Date:  2016-07-01       Impact factor: 2.333

5.  How Water's Properties Are Encoded in Its Molecular Structure and Energies.

Authors:  Emiliano Brini; Christopher J Fennell; Marivi Fernandez-Serra; Barbara Hribar-Lee; Miha Lukšič; Ken A Dill
Journal:  Chem Rev       Date:  2017-09-26       Impact factor: 60.622

6.  The influence of solid state information and descriptor selection on statistical models of temperature dependent aqueous solubility.

Authors:  Richard L Marchese Robinson; Kevin J Roberts; Elaine B Martin
Journal:  J Cheminform       Date:  2018-08-29       Impact factor: 5.514

7.  Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges.

Authors:  Ádám Ganyecz; Mihály Kállay
Journal:  J Phys Chem A       Date:  2022-04-08       Impact factor: 2.944

  7 in total

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