Literature DB >> 26592290

Multiscale Modeling of Chemistry in Water: Are We There Yet?

Rosa E Bulo1,2, Carine Michel1, Paul Fleurat-Lessard1, Philippe Sautet1.   

Abstract

This paper critically evaluates the state of the art in combined quantum mechanical/molecular mechanical (QM/MM) approaches to the computational description of chemistry in water and supplies guidelines for the setup of customized multiscale simulations of aqueous processes. We differentiate between structural and dynamic performance, since some tasks, e.g., the reproduction of NMR or UV-vis spectra, require only structural accuracy, while others, i.e., reaction mechanisms, require accurate dynamic data as well. As a model system for aqueous solutions in general, the approaches were tested on a QM water cluster in an environment of MM water molecules. The key difficulty is the description of the possible diffusion of QM molecules into the MM region and vice versa. The flexible inner region ensemble separator (FIRES) approach constrains QM solvent molecules within an active (QM) region. Sorted adaptive partitioning (SAP), difference-based adaptive solvation (DAS), and buffered-force (BF) are all adaptive approaches that use a buffer zone in which solvent molecules gradually adapt from QM to MM (or vice versa). The costs of SAP and DAS are relatively high, while BF is fast but sacrifices conservation of both energy and momentum. Simulations in the limit of an infinitely small buffer zone, where DAS and SAP become equivalent, are discussed as well and referred to as ABRUPT. The best structural accuracy is obtained with DAS, BF, and ABRUPT, all three of similar quality. FIRES performs very well for dynamic properties localized deep within the QM region. By means of elimination DAS emerges as the best overall compromise between structural and dynamic performance. Eliminating the buffer zone (ABRUPT) improves efficiency and still leads to surprisingly good results. While none of the many new flavors are perfect, all together this new field already allows accurate description of a wide range of structural and dynamic properties of aqueous solutions.

Entities:  

Year:  2013        PMID: 26592290     DOI: 10.1021/ct4005596

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


  11 in total

1.  Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM.

Authors:  Jia-Ning Wang; Wei Liu; Pengfei Li; Yan Mo; Wenxin Hu; Jun Zheng; Xiaoliang Pan; Yihan Shao; Ye Mei
Journal:  J Chem Theory Comput       Date:  2021-02-16       Impact factor: 6.006

2.  A Many-Body, Fully Polarizable Approach to QM/MM Simulations.

Authors:  Eleftherios Lambros; Filippo Lipparini; Gerardo Andrés Cisneros; Francesco Paesani
Journal:  J Chem Theory Comput       Date:  2020-11-19       Impact factor: 6.006

3.  Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory.

Authors:  Joani Mato; Adam W Duster; Emilie B Guidez; Hai Lin
Journal:  J Chem Theory Comput       Date:  2021-08-27       Impact factor: 6.578

Review 4.  Enhanced semiempirical QM methods for biomolecular interactions.

Authors:  Nusret Duygu Yilmazer; Martin Korth
Journal:  Comput Struct Biotechnol J       Date:  2015-02-28       Impact factor: 7.271

5.  The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.

Authors:  Letif Mones; Andrew Jones; Andreas W Götz; Teodoro Laino; Ross C Walker; Ben Leimkuhler; Gábor Csányi; Noam Bernstein
Journal:  J Comput Chem       Date:  2015-02-03       Impact factor: 3.376

6.  Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges.

Authors:  Ivan Carnimeo; Chiara Cappelli; Vincenzo Barone
Journal:  J Comput Chem       Date:  2015-09-24       Impact factor: 3.376

7.  Explicit Solvation Matters: Performance of QM/MM Solvation Models in Nucleophilic Addition.

Authors:  Jelle M Boereboom; Paul Fleurat-Lessard; Rosa E Bulo
Journal:  J Chem Theory Comput       Date:  2018-03-16       Impact factor: 6.006

8.  Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method.

Authors:  Hiroshi C Watanabe
Journal:  Molecules       Date:  2018-07-27       Impact factor: 4.411

9.  Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard⁻Jones Parameters for Water and to Study Solvation of TiO₂ Nanoparticles.

Authors:  Asmus Ougaard Dohn; Daniele Selli; Gianluca Fazio; Lorenzo Ferraro; Jens Jørgen Mortensen; Bartolomeo Civalleri; Cristiana Di Valentin
Journal:  Molecules       Date:  2018-11-13       Impact factor: 4.411

Review 10.  Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

Authors:  Gerardo Andrés Cisneros; Kjartan Thor Wikfeldt; Lars Ojamäe; Jibao Lu; Yao Xu; Hedieh Torabifard; Albert P Bartók; Gábor Csányi; Valeria Molinero; Francesco Paesani
Journal:  Chem Rev       Date:  2016-05-17       Impact factor: 60.622

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