Literature DB >> 32588851

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

Mattia Bondanza1, Michele Nottoli1, Lorenzo Cupellini1, Filippo Lipparini1, Benedetta Mennucci1.   

Abstract

Nowadays, hybrid QM/MM approaches are widely used to study (supra)molecular systems embedded in complex biological matrices. However, in their common formulation, mutual interactions between the quantum and classical parts are neglected. To go beyond such a picture, a polarizable embedding can be used. In this perspective, we focus on the induced point dipole formulation of polarizable QM/MM approaches and we show how efficient and linear scaling implementations have allowed their application to the modeling of complex biosystems. In particular, we discuss their use in the prediction of spectroscopies and in molecular dynamics simulations, including Born-Oppenheimer dynamics, enhanced sampling techniques and nonadiabatic descriptions. We finally suggest the theoretical and computational developments that still need to be achieved to overcome the limitations which have prevented so far larger diffusion of these methods.

Year:  2020        PMID: 32588851     DOI: 10.1039/d0cp02119a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  13 in total

1.  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

2.  Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex.

Authors:  Lorenzo Cupellini; Pu Qian; Tu C Nguyen-Phan; Alastair T Gardiner; Richard J Cogdell
Journal:  Photosynth Res       Date:  2022-06-08       Impact factor: 3.573

Review 3.  Recent progress in atomistic modeling of light-harvesting complexes: a mini review.

Authors:  Sayan Maity; Ulrich Kleinekathöfer
Journal:  Photosynth Res       Date:  2022-10-07       Impact factor: 3.429

4.  Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges.

Authors:  WanZhen Liang; Zheng Pei; Yuezhi Mao; Yihan Shao
Journal:  J Chem Phys       Date:  2022-06-07       Impact factor: 4.304

5.  Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

Authors:  Qiang Cui; Tanmoy Pal; Luke Xie
Journal:  J Phys Chem B       Date:  2021-01-06       Impact factor: 2.991

6.  Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.

Authors:  Jorge Nochebuena; Sehr Naseem-Khan; G Andrés Cisneros
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2021-01-12

7.  BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations.

Authors:  Bettina Lier; Peter Poliak; Philipp Marquetand; Julia Westermayr; Chris Oostenbrink
Journal:  J Phys Chem Lett       Date:  2022-04-25       Impact factor: 6.888

8.  Computational Investigation of Structural and Spectroscopic Properties of LOV-Based Proteins with Improved Fluorescence.

Authors:  Felipe Cardoso Ramos; Lorenzo Cupellini; Benedetta Mennucci
Journal:  J Phys Chem B       Date:  2021-02-10       Impact factor: 2.991

9.  How Can We Predict Accurate Electrochromic Shifts for Biochromophores? A Case Study on the Photosynthetic Reaction Center.

Authors:  Abhishek Sirohiwal; Frank Neese; Dimitrios A Pantazis
Journal:  J Chem Theory Comput       Date:  2021-02-10       Impact factor: 6.006

10.  Probing aqueous ions with non-local Auger relaxation.

Authors:  Geethanjali Gopakumar; Eva Muchová; Isaak Unger; Sebastian Malerz; Florian Trinter; Gunnar Öhrwall; Filippo Lipparini; Benedetta Mennucci; Denis Céolin; Carl Caleman; Iain Wilkinson; Bernd Winter; Petr Slavíček; Uwe Hergenhahn; Olle Björneholm
Journal:  Phys Chem Chem Phys       Date:  2022-04-13       Impact factor: 3.676

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