1
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Song C, Wang LP. A Polarizable QM/MM Model That Combines the State-Averaged CASSCF and AMOEBA Force Field for Photoreactions in Proteins. J Chem Theory Comput 2024. [PMID: 39088696 DOI: 10.1021/acs.jctc.4c00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
This study presents the polarizable quantum mechanics/molecular mechanics (QM/MM) embedding of the state-averaged complete active space self-consistent field (SA-CASSCF) in the atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field for the purpose of studying photoreactions in protein environments. We describe two extensions of our previous work that combine SA-CASSCF with AMOEBA water models, allowing it to be generalized to AMOEBA models for proteins and other macromolecules. First, we discuss how our QM/MM model accounts for the discrepancy between the direct and polarization electric fields that arises in the AMOEBA description of intramolecular polarization. A second improvement is the incorporation of link atom schemes to treat instances in which the QM/MM boundary goes through covalent bonds. A single-link atom scheme and double-link atom scheme are considered in this work, and we will discuss how electrostatic interaction, van der Waals interaction, and various kinds of valence terms are treated across the boundary. To test the accuracy of the link atom scheme, we will compare QM/MM with full QM calculations and study how the errors in ground state properties, excited state properties, and excitation energies change when tuning the parameters in the link atom scheme. We will also test the new SA-CASSCF/AMOEBA method on an elementary reaction step in NanoLuc, an artificial bioluminescence luciferase. We will show how the reaction mechanism is different when calculated in the gas phase, in polarizable continuum medium (PCM), versus in protein AMOEBA models.
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Affiliation(s)
- Chenchen Song
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
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2
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Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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3
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Capone M, Romanelli M, Castaldo D, Parolin G, Bello A, Gil G, Vanzan M. A Vision for the Future of Multiscale Modeling. ACS PHYSICAL CHEMISTRY AU 2024; 4:202-225. [PMID: 38800726 PMCID: PMC11117712 DOI: 10.1021/acsphyschemau.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, L’Aquila 67010, Italy
| | - Marco Romanelli
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Davide Castaldo
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Giovanni Parolin
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Alessandro Bello
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gabriel Gil
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Instituto
de Cibernética, Matemática y Física (ICIMAF), La Habana 10400, Cuba
| | - Mirko Vanzan
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, University of Milano, Milano 20133, Italy
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4
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Nochebuena J, Simmonett AC, Cisneros GA. Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP. J Chem Phys 2024; 160:174103. [PMID: 38747990 PMCID: PMC11223170 DOI: 10.1063/5.0200722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/14/2024] [Indexed: 07/06/2024] Open
Abstract
Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents a novel implementation of the Gaussian Electrostatic Model (GEM), a polarizable density-based force field, within the QM/MM framework. This advancement provides seamless integration, enabling efficient and optimized QM/GEM calculations in a single step using the LICHEM Code. We have successfully applied our implementation to water dimers and hexamers, demonstrating the ability to handle water systems with varying numbers of water molecules. Moreover, we have extended the application to describe the double proton transfer of the aspartic acid dimer in a box of water, which highlights the method's proficiency in investigating heterogeneous systems. Our implementation offers the flexibility to perform on-the-fly density fitting or to utilize pre-fitted coefficients to estimate exchange and Coulomb contributions. This flexibility enhances efficiency and accuracy in modeling molecular interactions, especially in systems where polarization effects are significant.
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Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Andrew C. Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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5
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Bondanza M, Nottoli T, Nottoli M, Cupellini L, Lipparini F, Mennucci B. The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics. J Chem Phys 2024; 160:134106. [PMID: 38557842 DOI: 10.1063/5.0198251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
We present a new library designed to provide a simple and straightforward way to implement QM/AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) and other polarizable QM/MM (Molecular Mechanics) methods based on induced point dipoles. The library, herein referred to as OpenMMPol, is free and open-sourced and is engineered to address the increasing demand for accurate and efficient QM/MM simulations. OpenMMPol is specifically designed to allow polarizable QM/MM calculations of ground state energies and gradients and excitation properties. Key features of OpenMMPol include a modular architecture facilitating extensibility, parallel computing capabilities for enhanced performance on modern cluster architectures, a user-friendly interface for intuitive implementation, and a simple and flexible structure for providing input data. To show the capabilities offered by the library, we present an interface with PySCF to perform QM/AMOEBA molecular dynamics, geometry optimization, and excited-state calculation based on (time-dependent) density functional theory.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Tommaso Nottoli
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Michele Nottoli
- Institute of Applied Analysis and Numerical Simulation, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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6
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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7
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Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
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8
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Jónsson EÖ, Rasti S, Galynska M, Meyer J, Jónsson H. Transferable Potential Function for Flexible H 2O Molecules Based on the Single-Center Multipole Expansion. J Chem Theory Comput 2022; 18:7528-7543. [PMID: 36395502 DOI: 10.1021/acs.jctc.2c00598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A potential function is presented for describing a system of flexible H2O molecules based on the single-center multipole expansion (SCME) of the electrostatic interaction. The model, referred to as SCME/f, includes the variation of the molecular quadrupole moment as well as the dipole moment with changes in bond length and angle so as to reproduce results of high-level electronic structure calculations. The multipole expansion also includes fixed octupole and hexadecapole moments, as well as anisotropic dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole polarizability tensors. The model contains five adjustable parameters related to the repulsive interaction and damping functions in the electrostatic and dispersion interactions. Their values are adjusted to reproduce the lowest energy isomers of small clusters, (H2O)n with n = 2-6, as well as measured properties of the ice Ih crystal. Subsequent calculations of the energy difference between the various isomer configurations of the clusters show that SCME/f gives good agreement with results of electronic structure calculations and represents a significant improvement over the previously presented rigid SCME potential function. Analysis of the vibrational frequencies of the clusters and structural properties of ice Ih crystal show the importance of accurately describing the variation of the quadrupole moment with molecular structures.
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Affiliation(s)
- Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
| | - Soroush Rasti
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RALeiden, The Netherlands
| | - Marta Galynska
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
| | - Jörg Meyer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RALeiden, The Netherlands
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
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9
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Creutzberg J, Hedegård ED. Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks. J Chem Theory Comput 2022; 18:3671-3686. [PMID: 35549262 DOI: 10.1021/acs.jctc.1c01249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Explicit embedding methods combined with the complex polarization propagator (CPP) enable the modeling of spectroscopy for increasingly complex systems with a high density of states. We present the first derivation and implementation of the CPP in four- and exact-two-component (X2C) polarizable embedding (PE) frameworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP, respectively. We illustrate the methods by estimating the solvent effect on ultraviolet-visible (UV-vis) and X-ray atomic absorption (XAS) spectra of [Rh(H2O)6]3+ and [Ir(H2O)6]3+ immersed in aqueous solution. We moreover estimate solvent effects on UV-vis spectra of a platinum complex that can be photochemically activated (in water) to kill cancer cells. Our results clearly show that the inclusion of the environment is required: UV-vis and (to a lesser degree) XAS spectra can become qualitatively different from vacuum calculations. Comparison of PE-4c-CPP and PE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect obtained with the 4c methods.
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Affiliation(s)
- Joel Creutzberg
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden
| | - Erik D Hedegård
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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10
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Cignoni E, Slama V, Cupellini L, Mennucci B. The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol. J Chem Phys 2022; 156:120901. [DOI: 10.1063/5.0086275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Slama
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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11
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Qu X, Dong L, Si Y, Zhao Y, Wang Q, Su P, Wang B. Reliable Prediction of the Protein-Ligand Binding Affinity Using a Charge Penetration Corrected AMOEBA Force Field: A Case Study of Drug Resistance Mutations in Abl Kinase. J Chem Theory Comput 2022; 18:1692-1700. [PMID: 35107298 DOI: 10.1021/acs.jctc.1c01005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein mutations that directly impair drug binding are related to therapeutic resistance, and accurate prediction of their impact on drug binding would benefit drug design and clinical practice. Here, we have developed a scoring strategy that predicts the effect of the mutations on the protein-ligand binding affinity. In view of the critical importance of electrostatics in protein-ligand interactions, the charge penetration corrected AMOEBA force field (AMOEBA_CP model) was employed to improve the accuracy of the calculated electrostatic energy. We calculated the electrostatic energy using an energy decomposition analysis scheme based on the generalized Kohn-Sham (GKS-EDA). The AMOEBA_CP model was validated by a protein-fragment-ligand complex data set (Abl236) constructed from the co-crystal structures of the cancer target Abl kinase with six inhibitors. To predict ligand binding affinity changes upon protein mutation of Abl kinase, we used sampling protocol with multistep simulated annealing to search conformations of mutant proteins. The scoring strategy based on AMOEBA_CP model has achieved considerable performance in predicting resistance for 8 kinase inhibitors across 144 clinically identified point mutations. Overall, this study illustrates that the AMOEBA_CP model, which accurately treats electrostatics through penetration correction, enables the accurate prediction of the mutation-induced variation of protein-ligand binding affinity.
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Affiliation(s)
- Xiaoyang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Lina Dong
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yubing Si
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, P. R. China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Peifeng Su
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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12
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Lambros E, Dasgupta S, Palos E, Swee S, Hu J, Paesani F. General Many-Body Framework for Data-Driven Potentials with Arbitrary Quantum Mechanical Accuracy: Water as a Case Study. J Chem Theory Comput 2021; 17:5635-5650. [PMID: 34370954 DOI: 10.1021/acs.jctc.1c00541] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general framework for the development of data-driven many-body (MB) potential energy functions (MB-QM PEFs) that represent the interactions between small molecules at an arbitrary quantum-mechanical (QM) level of theory. As a demonstration, a family of MB-QM PEFs for water is rigorously derived from density functionals belonging to different rungs across Jacob's ladder of approximations within density functional theory (MB-DFT) and from Møller-Plesset perturbation theory (MB-MP2). Through a systematic analysis of individual MB contributions to the interaction energies of water clusters, we demonstrate that all MB-QM PEFs preserve the same accuracy as the corresponding ab initio calculations, with the exception of those derived from density functionals within the generalized gradient approximation (GGA). The differences between the DFT and MB-DFT results are traced back to density-driven errors that prevent GGA functionals from accurately representing the underlying molecular interactions for different cluster sizes and hydrogen-bonding arrangements. We show that this shortcoming may be overcome, within the MB formalism, by using density-corrected functionals (DC-DFT) that provide a more consistent representation of each individual MB contribution. This is demonstrated through the development of a MB-DFT PEF derived from DC-PBE-D3 data, which more accurately reproduce the corresponding ab initio results.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Steven Swee
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jie Hu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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13
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Loco D, Lagardère L, Adjoua O, Piquemal JP. Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity. Acc Chem Res 2021; 54:2812-2822. [PMID: 33961401 PMCID: PMC8264944 DOI: 10.1021/acs.accounts.0c00662] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/20/2022]
Abstract
The computational modeling of realistic extended systems, relevant in, e.g., Chemistry and Biophysics, is a fundamental problem of paramount importance in contemporary research. Enzymatic catalysis and photoinduced processes in pigment-protein complexes are typical problems targeted by computer-aided approaches, to complement experiments as interpretative tools at a molecular scale. The daunting complexity of this task lies in between the opposite stringent requirements of results' reliability for structural/dynamical properties and related intermolecular interactions, and a mandatory principle of realism in the modeling strategy. Therefore, in practice, a truly realistic computational model of a biologically relevant system can easily fail to meet the accuracy requirement, in order to balance the excessive computational cost necessary to reach the desired precision.To address such an "accuracy vs reality" dualistic requirement, mixed quantum mechanics/classical mechanics approaches within Atomistic (i.e., preserving the discrete particle configuration) Polarizable Embeddings (QM/APEs) methods have been proposed over the years. In this Account, we review recent developments in the design and application of general QM/APE methods, targeting situations where a local intrinsically quantum behavior is coupled to a large molecular system (i.e., an environment), often involving processes with different dynamical time scales, in order to avoid brute-force, unpractical quantum chemistry calculations on the complete system.In the first place, our interest is devoted to the available APEs models presently implemented in computational software, highlighting the quantum chemistry methods that can be used to treat the QM subsystem. We review the coupling strategy between the QM subsystem and the APE, which requires to examine the way the QM/MM mutual interactions are accounted for and how the polarization of the classical environment is considered with respect to (wrt) the quantum variables. Because of the need of reliable molecular and macromolecular structures, a pivotal aspect to address here is the handling of the system dynamics (i.e., gradients wrt nuclear positions are required), especially for large molecular assemblies composed by an overwhelming number of atoms, exploring many conformations on a complex energy landscape.Alongside, we highlight our views on the necessary steps to take toward more accurate general-purposes and transferable explicit embeddings. The main objective to achieve here is to design a more physically grounded multiscale approach. To do so, one should apply advanced new generation classical models to account for refined induction effects that are able to (i) improve the quality of QM/MM interaction energies; (ii) enhance transferability by avoiding the compulsory partial (or total) reparameterization of the classical model. Moreover, the extension of recent developments originating from the field of advanced classical molecular dynamics (MD) to the realm of QM/APE methods is a key direction to improve both speed and efficiency for the phase space exploration of systems of growing size and complexity.Lastly, we point out specific research topics where an advanced QM/APE dynamics can certainly shed some light. For example, we discuss chemical reactions in "harsh" environments and the case of spectroscopic theoretical modeling where the inclusion of refined environment effects is often mandatory.
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Affiliation(s)
- Daniele Loco
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Intitut
Parisien de Chimie Physique et Théorique, Sorbonne Université, FR 2622 CNRS, 75005 Paris, France
| | - Olivier Adjoua
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Institut
Universitaire de France, F-75005 Paris, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
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14
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Nochebuena J, Naseem-Khan S, Cisneros GA. Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1515. [PMID: 34367343 PMCID: PMC8341087 DOI: 10.1002/wcms.1515] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/19/2020] [Indexed: 01/02/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and biological systems. The combination of QM and MM methods to represent a system gives rise to several challenges that need to be addressed. The increase in computational speed has allowed the expanded use of more complicated and accurate methods for both QM and MM simulations. Here, we review some approaches that address several common challenges encountered in QM/MM simulations with advanced polarizable potentials, from methods to account for boundary across covalent bonds and long-range effects, to polarization and advanced embedding potentials.
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Affiliation(s)
- Jorge Nochebuena
- Department of Chemistry, University of North Texas, Denton, Texas, USA
| | - Sehr Naseem-Khan
- Department of Chemistry, University of North Texas, Denton, Texas, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, USA
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15
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Wappett DA, Goerigk L. A guide to benchmarking enzymatically catalysed reactions: the importance of accurate reference energies and the chemical environment. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02770-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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Nottoli M, Bondanza M, Lipparini F, Mennucci B. An enhanced sampling QM/AMOEBA approach: The case of the excited state intramolecular proton transfer in solvated 3-hydroxyflavone. J Chem Phys 2021; 154:184107. [PMID: 34241028 DOI: 10.1063/5.0046844] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We present an extension of the polarizable quantum mechanical (QM)/AMOEBA approach to enhanced sampling techniques. This is achieved by connecting the enhanced sampling PLUMED library to the machinery based on the interface of Gaussian and Tinker to perform QM/AMOEBA molecular dynamics. As an application, we study the excited state intramolecular proton transfer of 3-hydroxyflavone in two solvents: methanol and methylcyclohexane. By using a combination of molecular dynamics and umbrella sampling, we find an ultrafast component of the transfer, which is common to the two solvents, and a much slower component, which is active in the protic solvent only. The mechanisms of the two components are explained in terms of intramolecular vibrational redistribution and intermolecular hydrogen-bonding, respectively. Ground and excited state free energies along an effective reaction coordinate are finally obtained allowing for a detailed analysis of the solvent mediated mechanism.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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17
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Nottoli M, Cupellini L, Lipparini F, Granucci G, Mennucci B. Multiscale Models for Light-Driven Processes. Annu Rev Phys Chem 2021; 72:489-513. [PMID: 33561359 DOI: 10.1146/annurev-physchem-090419-104031] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
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18
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Nottoli M, Lipparini F. General formulation of polarizable embedding models and of their coupling. J Chem Phys 2020; 153:224108. [PMID: 33317291 DOI: 10.1063/5.0035165] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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19
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Lambros E, Lipparini F, Cisneros GA, Paesani F. A Many-Body, Fully Polarizable Approach to QM/MM Simulations. J Chem Theory Comput 2020; 16:7462-7472. [PMID: 33213149 PMCID: PMC8131112 DOI: 10.1021/acs.jctc.0c00932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-mechanical contributions (e.g., exchange-repulsion and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit two-body and three-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 two-body and three-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.
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Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | | | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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20
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Nottoli M, Mennucci B, Lipparini F. Excited state Born-Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA. Phys Chem Chem Phys 2020; 22:19532-19541. [PMID: 32844823 DOI: 10.1039/d0cp03688a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We present the implementation of excited state Born-Oppenheimer molecular dynamics (BOMD) using a polarizable QM/MM approach based on a time-dependent density functional theory (TDDFT) formulation and the AMOEBA force field. The implementation relies on an interface between Tinker and Gaussian software and it uses an algorithm for the calculation of QM/MM energy and forces which scales linearly with the number of MM atoms. The resulting code can perform TDDFT/AMOEBA BOMD simulations on real-life systems with standard computational resources. As a test case, the method is applied to the study of the mechanism of locally-excited to charge-transfer conversion in dimethylaminobenzonitrile in a polar solvent. Our simulations confirm that such a conversion is governed by the twisting of the dimethylamino group which is accompanied by an important reorientation of solvent molecules.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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21
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Kraus J, Gupta R, Lu M, Gronenborn AM, Akke M, Polenova T. Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter. Chemphyschem 2020; 21:1436-1443. [PMID: 32363727 PMCID: PMC8080305 DOI: 10.1002/cphc.202000249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Indexed: 01/07/2023]
Abstract
Chemical shift tensors obtained from solid-state NMR spectroscopy are very sensitive reporters of structure and dynamics in proteins. While accurate 13 C and 15 N chemical shift tensors are accessible by magic angle spinning (MAS) NMR, their quantum mechanical calculations remain challenging, particularly for 15 N atoms. Here we compare experimentally determined backbone 13 Cα and 15 NH chemical shift tensors by MAS NMR with hybrid quantum mechanics/molecular mechanics/molecular dynamics (MD-QM/MM) calculations for the carbohydrate-binding domain of galectin-3. Excellent agreement between experimental and computed 15 NH chemical shift anisotropy values was obtained using the Amber ff15ipq force field when solvent dynamics was taken into account in the calculation. Our results establish important benchmark conditions for improving the accuracy of chemical shift calculations in proteins and may aid in the validation of protein structure models derived by MAS NMR.
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Affiliation(s)
- Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Department of Chemistry, The College of Staten Island, 2800 Victory Blvd, Staten Island, NY 10314
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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22
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Prentice JCA, Aarons J, Womack JC, Allen AEA, Andrinopoulos L, Anton L, Bell RA, Bhandari A, Bramley GA, Charlton RJ, Clements RJ, Cole DJ, Constantinescu G, Corsetti F, Dubois SMM, Duff KKB, Escartín JM, Greco A, Hill Q, Lee LP, Linscott E, O'Regan DD, Phipps MJS, Ratcliff LE, Serrano ÁR, Tait EW, Teobaldi G, Vitale V, Yeung N, Zuehlsdorff TJ, Dziedzic J, Haynes PD, Hine NDM, Mostofi AA, Payne MC, Skylaris CK. The ONETEP linear-scaling density functional theory program. J Chem Phys 2020; 152:174111. [PMID: 32384832 DOI: 10.1063/5.0004445] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.
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Affiliation(s)
- Joseph C A Prentice
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Jolyon Aarons
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - James C Womack
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Alice E A Allen
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lampros Andrinopoulos
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Lucian Anton
- UKAEA, Culham Science Centre, Abingdon OX14 3DB, United Kingdom
| | - Robert A Bell
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Arihant Bhandari
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Gabriel A Bramley
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Robert J Charlton
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Rebecca J Clements
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Gabriel Constantinescu
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Fabiano Corsetti
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Simon M-M Dubois
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Kevin K B Duff
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - José María Escartín
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Andrea Greco
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Quintin Hill
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Louis P Lee
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Edward Linscott
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - David D O'Regan
- School of Physics, AMBER, and CRANN Institute, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Maximillian J S Phipps
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Laura E Ratcliff
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Álvaro Ruiz Serrano
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Edward W Tait
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Gilberto Teobaldi
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Valerio Vitale
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Nelson Yeung
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Peter D Haynes
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Arash A Mostofi
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Mike C Payne
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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23
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Bradshaw RT, Dziedzic J, Skylaris CK, Essex JW. The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields? J Chem Inf Model 2020; 60:3131-3144. [DOI: 10.1021/acs.jcim.0c00217] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Richard T. Bradshaw
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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24
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Ding Y, Xu Y, Qian C, Chen J, Zhu J, Huang H, Shi Y, Huang J. Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields. J Comput Aided Mol Des 2020; 34:421-435. [PMID: 31960252 DOI: 10.1007/s10822-020-00282-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022]
Abstract
The water-octanol partition coefficient is an important physicochemical property for small molecule drug design. Here, we report our participation in the SAMPL6 logP prediction challenge with free energy perturbation (FEP) calculations in the water phase and in the 1-octanol phase using Drude polarizable force fields. Root mean square error (RMSE) and mean absolute error (MAE) of our prediction are equal to 1.85 and 1.25 logP units. The errors are not evenly distributed. Out of eleven SAMPL6 solutes, FEP/Drude performed very badly on three molecules (deviations all larger than 2 logP units) but good on the remaining eight (deviations all less than 1 logP unit). We find while FEP converges well within one nanosecond in water, simulations in 1-octanol need much longer simulation time and possibly more independent runs for sampling. We also find out that 1-octanol, albeit being a non-polar solvent, still polarizes solute molecules and forms stable hydrogen bonds with them. At the end, we attempt to reweight FEP trajectories with QM/Drude calculations and discuss possible caveats in our simulation setup.
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Affiliation(s)
- Ye Ding
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - You Xu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Cheng Qian
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jinfeng Chen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jian Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Houhou Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Yi Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China. .,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
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25
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Quantum mechanics/molecular mechanics multiscale modeling of biomolecules. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2020. [DOI: 10.1016/bs.apoc.2020.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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Bondanza M, Nottoli M, Cupellini L, Lipparini F, Mennucci B. Polarizable embedding QM/MM: the future gold standard for complex (bio)systems? Phys Chem Chem Phys 2020; 22:14433-14448. [DOI: 10.1039/d0cp02119a] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We provide a perspective of the induced dipole formulation of polarizable QM/MM, showing how efficient implementations will enable their application to the modeling of dynamics, spectroscopy, and reactivity in complex biosystems.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
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27
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Jónsson EÖ, Dohn AO, Jónsson H. Polarizable Embedding with a Transferable H 2O Potential Function I: Formulation and Tests on Dimer. J Chem Theory Comput 2019; 15:6562-6577. [PMID: 31689104 DOI: 10.1021/acs.jctc.9b00777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The incorporation of mutual polarization in multiscale simulations where different regions of the system are treated at different level of theory is important in studies of, for example, electronic excitations and charge transfer processes. We present here an energy functional for describing a quantum mechanics/molecular mechanics (QM/MM) scheme that includes reciprocal polarization between the two subsystems. The inclusion of polarization alleviates shortcomings inherent in electrostatic embedding QM/MM models based on point-charge force fields. A density functional theory (DFT) description of the QM subsystem is coupled to a single center multipole expansion (SCME) description of H2O molecules in the MM subsystem that includes anisotropic dipole and quadrupole polarizability as well as static multipoles up to and including the hexadecapole. The energy functional and the coupling scheme is general and can be extended to arbitrary order in terms of both the static and induced moments. Tests of the energy surface for the H2O dimer show that the QM/MM results lie in between the pure DFT and pure SCME values. The consistency of the many-body contributions to the energy and analytical forces is demonstrated for an H2O pentamer.
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Affiliation(s)
- Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, VR-III , University of Iceland , Reykjavík 107 , Iceland
| | - Asmus Ougaard Dohn
- Science Institute and Faculty of Physical Sciences, VR-III , University of Iceland , Reykjavík 107 , Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, VR-III , University of Iceland , Reykjavík 107 , Iceland
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28
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Giovannini T, Grazioli L, Ambrosetti M, Cappelli C. Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles. J Chem Theory Comput 2019; 15:5495-5507. [DOI: 10.1021/acs.jctc.9b00574] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Laura Grazioli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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29
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Loco D, Lagardère L, Cisneros GA, Scalmani G, Frisch M, Lipparini F, Mennucci B, Piquemal JP. Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings. Chem Sci 2019; 10:7200-7211. [PMID: 31588288 PMCID: PMC6677116 DOI: 10.1039/c9sc01745c] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/08/2019] [Indexed: 12/17/2022] Open
Abstract
In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born-Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.
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Affiliation(s)
- Daniele Loco
- Sorbonne Université , CNRS , Laboratoire de Chimie Théorique, LCT , Paris , France . ;
| | - Louis Lagardère
- Sorbonne Université , CNRS , Institut Parisien de Chimie Physique et Théorique, IP2CT , Paris , France
- Sorbonne Université , Institut des Sciences du Calcul et des Données, ISCD , Paris , France
| | | | | | | | - Filippo Lipparini
- Univerisita di Pisa , Dipartimento di Chimica e ChimicaIndustriale , Pisa , Italy
| | - Benedetta Mennucci
- Univerisita di Pisa , Dipartimento di Chimica e ChimicaIndustriale , Pisa , Italy
| | - Jean-Philip Piquemal
- Sorbonne Université , CNRS , Laboratoire de Chimie Théorique, LCT , Paris , France . ;
- Institut Universitaire de France, IUF , Paris , France
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
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30
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Lipparini F. General Linear Scaling Implementation of Polarizable Embedding Schemes. J Chem Theory Comput 2019; 15:4312-4317. [PMID: 31348655 DOI: 10.1021/acs.jctc.9b00585] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A general framework to treat polarizable embedding schemes in the context of QM/MM calculations is presented. Such a framework is completely general, as it allows in principle one to treat any electrostatic distribution and polarization model with minimal modifications and achieves linear scaling in computational cost and memory requirements. The performances and scaling of the new implementation are demonstrated with benchmark calculations on water clusters including up to 1146240 atoms.
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Affiliation(s)
- Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy
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31
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Dziedzic J, Head-Gordon T, Head-Gordon M, Skylaris CK. Mutually polarizable QM/MM model with in situ optimized localized basis functions. J Chem Phys 2019; 150:074103. [PMID: 30795653 DOI: 10.1063/1.5080384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem - with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repulsive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl-. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface.
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Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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32
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Wildman A, Donati G, Lipparini F, Mennucci B, Li X. Nonequilibrium Environment Dynamics in a Frequency-Dependent Polarizable Embedding Model. J Chem Theory Comput 2018; 15:43-51. [PMID: 30512961 DOI: 10.1021/acs.jctc.8b00836] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) models are some of the most powerful and computationally feasible approaches to account for solvent effects or more general environmental perturbations on quantum chemical systems. In their more recent formulations (known as polarizable embedding) they can account for electrostatic and mutual polarization effects between the QM and the MM subsystems. In this paper, a polarizable embedding scheme based on induced dipoles that is able both to describe electron evolution of the embedded QM system in an efficient manner as well as to capture the frequency dependent behavior of the solvent is proposed, namely, ωMMPol. The effects of this frequency-dependent solvent on a time-dependent model system-the Rabi oscillations of H2+ in a resonant field-are considered. The solvent is shown to introduce only mild perturbations when the excitation frequencies of the solvent and the solute are off-resonant. However, the dynamics of the H2+ are fundamentally changed in the presence of a near-resonant excitation solvent. The effectiveness of ωMMPol to simulating realistic chemical systems is demonstrated by capturing charge transfer dynamics within a solvated system.
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Affiliation(s)
- Andrew Wildman
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Greta Donati
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale , Universitá di Pisa , Via Risorgimento 35 , 56126 Pisa , Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , Universitá di Pisa , Via Risorgimento 35 , 56126 Pisa , Italy
| | - Xiaosong Li
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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33
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König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules 2018; 23:E2695. [PMID: 30347691 PMCID: PMC6222909 DOI: 10.3390/molecules23102695] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/01/2022] Open
Abstract
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
- School of Life Sciences, Westlake University, 18 Shilongshan Street, Hangzhou 310024, China.
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Alexander D MacKerell
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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34
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Pan X, Rosta E, Shao Y. Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations. Molecules 2018; 23:E2500. [PMID: 30274290 PMCID: PMC6222767 DOI: 10.3390/molecules23102500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 11/16/2022] Open
Abstract
In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used explicitly in the evaluation of short-range QM/MM electrostatic interactions, while a multipolar representation for the QM electron density is employed to account for the long-range QM/MM electrostatic interactions. In order to avoid energy discontinuity at the cutoffs, which separate the short- and long-range QM/MM electrostatic interactions, a switching function should be utilized to ensure a smooth potential energy surface. In this study, we benchmarked the accuracy of such hybrid embedding schemes for QM/MM electrostatic interactions using different multipolar representations, switching functions and cutoff distances. For test systems (neutral and anionic oxyluciferin in MM (aqueous and enzyme) environments), the best accuracy was acquired with a combination of QM electrostatic potential (ESP) charges and dipoles and two switching functions (long-range electrostatic corrections (LREC) and Switch) in the treatment of long-range QM/MM electrostatics. It allowed us to apply a 10Å distance cutoff and still obtain QM/MM electrostatics/polarization energies within 0.1 kcal/mol and time-dependent density functional theory (TDDFT)/MM vertical excitation energies within 10-3 eV from theoretical reference values.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019⁻5251, USA.
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, UK.
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019⁻5251, USA.
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35
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Viquez Rojas CI, Fine J, Slipchenko LV. Exchange-repulsion energy in QM/EFP. J Chem Phys 2018; 149:094103. [PMID: 30195305 DOI: 10.1063/1.5043107] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The effective fragment potential (EFP) is a quantum mechanics (QM)-based model designed to accurately describe intermolecular interactions. Hybrid QM/EFP calculations combine quantum mechanical methods with an EFP embedding to study complex systems in which many-body effects are relevant. As in EFP-only calculations, non-bonded interactions between the QM region and EFP fragments are computed as a sum of electrostatic, polarization, dispersion, and exchange-repulsion energies. The exchange-repulsion term is a computational bottleneck of the EFP calculations. Here, we present a general procedure for computing the QM/EFP exchange-repulsion interactions based on one-electron contributions to the QM Hamiltonian, by using Gaussian functions to represent localized molecular orbitals of the effective fragments. The accuracy of the exchange-repulsion and total QM/EFP interaction energies is evaluated on a diverse set of dimers, including complexes from the S22 dataset of non-covalent interactions. In most cases, the QM/EFP energies are at least as accurate as corresponding EFP energies. A simple and computationally efficient form of the introduced QM/EFP exchange-repulsion term will facilitate further developments and applications of QM/EFP methods.
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Affiliation(s)
| | - Jonathan Fine
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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36
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37
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Huang J, Simmonett AC, Pickard FC, MacKerell AD, Brooks BR. Mapping the Drude polarizable force field onto a multipole and induced dipole model. J Chem Phys 2018; 147:161702. [PMID: 29096511 DOI: 10.1063/1.4984113] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The induced dipole and the classical Drude oscillator represent two major approaches for the explicit inclusion of electronic polarizability into force field-based molecular modeling and simulations. In this work, we explore the equivalency of these two models by comparing condensed phase properties computed using the Drude force field and a multipole and induced dipole (MPID) model. Presented is an approach to map the electrostatic model optimized in the context of the Drude force field onto the MPID model. Condensed phase simulations on water and 15 small model compounds show that without any reparametrization, the MPID model yields properties similar to the Drude force field with both models yielding satisfactory reproduction of a range of experimental values and quantum mechanical data. Our results illustrate that the Drude oscillator model and the point induced dipole model are different representations of essentially the same physical model. However, results indicate the presence of small differences between the use of atomic multipoles and off-center charge sites. Additionally, results on the use of dispersion particle mesh Ewald further support its utility for treating long-range Lennard Jones dispersion contributions in the context of polarizable force fields. The main motivation in demonstrating the transferability of parameters between the Drude and MPID models is that the more than 15 years of development of the Drude polarizable force field can now be used with MPID formalism without the need for dual-thermostat integrators nor self-consistent iterations. This opens up a wide range of new methodological opportunities for polarizable models.
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Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn St., Baltimore, Maryland 21201, USA
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 5635 Fishers Lane, Rockville, Maryland 20852, USA
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 5635 Fishers Lane, Rockville, Maryland 20852, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn St., Baltimore, Maryland 21201, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 5635 Fishers Lane, Rockville, Maryland 20852, USA
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38
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Ricardi N, Zech A, Gimbal-Zofka Y, Wesolowski TA. Explicit vs. implicit electronic polarisation of environment of an embedded chromophore in frozen-density embedding theory. Phys Chem Chem Phys 2018; 20:26053-26062. [DOI: 10.1039/c8cp05634j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparison of strategies to account for environment polarisation in Frozen Density Embedding Theory (FDET).
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Affiliation(s)
- Niccolò Ricardi
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Genève
- Switzerland
| | - Alexander Zech
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Genève
- Switzerland
| | - Yann Gimbal-Zofka
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Genève
- Switzerland
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39
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Nåbo LJ, Olsen JMH, Martínez TJ, Kongsted J. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein. J Chem Theory Comput 2017; 13:6230-6236. [DOI: 10.1021/acs.jctc.7b00528] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lina J. Nåbo
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Todd J. Martínez
- Department
of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94305, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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40
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Howard JC, Womack JC, Dziedzic J, Skylaris CK, Pritchard BP, Crawford TD. Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory. J Chem Theory Comput 2017; 13:5572-5581. [DOI: 10.1021/acs.jctc.7b00833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Coleman Howard
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - James C. Womack
- Department
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Jacek Dziedzic
- Department
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
- Faculty
of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- Department
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Benjamin P. Pritchard
- Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - T. Daniel Crawford
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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41
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Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal JP. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding. J Chem Theory Comput 2017; 13:4025-4033. [DOI: 10.1021/acs.jctc.7b00572] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniele Loco
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Louis Lagardère
- UPMC Univ. Paris
06, Institut des Sciences du Calcul et des Données, F-75005, Paris, France
| | - Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Jean-Philip Piquemal
- UPMC Univ. Paris
06, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Institut Universitaire de France, Paris
Cedex 05, 75231, France
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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42
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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43
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Milanese JM, Provorse MR, Alameda E, Isborn CM. Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent. J Chem Theory Comput 2017; 13:2159-2171. [DOI: 10.1021/acs.jctc.7b00159] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel M. Milanese
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Enrique Alameda
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California at Merced, Merced, California 95343, United States
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44
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Vitale V, Dziedzic J, Albaugh A, Niklasson AMN, Head-Gordon T, Skylaris CK. Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory. J Chem Phys 2017; 146:124115. [DOI: 10.1063/1.4978684] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Valerio Vitale
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Alex Albaugh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | | | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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45
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Huang J, Mei Y, König G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. J Chem Theory Comput 2017; 13:679-695. [PMID: 28081366 DOI: 10.1021/acs.jctc.6b01125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.
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Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States.,Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Gerhard König
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, NRW Germany, EU
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Frank C Pickard
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States.,Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
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