1
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Amblard D, Blase X, Duchemin I. Many-body GW calculations with very large scale polarizable environments made affordable: A fully ab initio QM/QM approach. J Chem Phys 2023; 159:164107. [PMID: 37873961 DOI: 10.1063/5.0168755] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
We present a many-body GW formalism for quantum subsystems embedded in discrete polarizable environments containing up to several hundred thousand atoms described at a fully ab initio random phase approximation level. Our approach is based on a fragment approximation in the construction of the Green's function and independent-electron susceptibilities. Further, the environing fragments susceptibility matrices are reduced to a minimal but accurate representation preserving low order polarizability tensors through a constrained minimization scheme. This approach dramatically reduces the cost associated with inverting the Dyson equation for the screened Coulomb potential W, while preserving the description of short to long-range screening effects. The efficiency and accuracy of the present scheme is exemplified in the paradigmatic cases of fullerene bulk, surface, subsurface, and slabs with varying number of layers.
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Affiliation(s)
- David Amblard
- Univ. Grenoble Alpes, CNRS, Institut NEEL, F-38042 Grenoble, France
| | - Xavier Blase
- Univ. Grenoble Alpes, CNRS, Institut NEEL, F-38042 Grenoble, France
| | - Ivan Duchemin
- Univ. Grenoble Alpes, CEA, IRIG-MEM-L_Sim, 38054 Grenoble, France
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2
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Jansen M, Reinholdt P, Hedegård ED, König C. Theoretical and Numerical Comparison of Quantum- and Classical Embedding Models for Optical Spectra. J Phys Chem A 2023. [PMID: 37399130 DOI: 10.1021/acs.jpca.3c02540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Quantum-mechanical (QM) and classical embedding models approximate a supermolecular quantum-chemical calculation. This is particularly useful when the supermolecular calculation has a size that is out of reach for present QM models. Although QM and classical embedding methods share the same goal, they approach this goal from different starting points. In this study, we compare the polarizable embedding (PE) and frozen-density embedding (FDE) models. The former is a classical embedding model, whereas the latter is a density-based QM embedding model. Our comparison focuses on solvent effects on optical spectra of solutes. This is a typical scenario where super-system calculations including the solvent environment become prohibitively large. We formulate a common theoretical framework for PE and FDE models and systematically investigate how PE and FDE approximate solvent effects. Generally, differences are found to be small, except in cases where electron spill-out becomes problematic in the classical frameworks. In these cases, however, atomic pseudopotentials can reduce the electron-spill-out issue.
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Affiliation(s)
- Marina Jansen
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstr. 3A, 30167 Hannover, Germany
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Erik D Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Carolin König
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstr. 3A, 30167 Hannover, Germany
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3
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Jaffrelot Inizan T, Plé T, Adjoua O, Ren P, Gökcan H, Isayev O, Lagardère L, Piquemal JP. Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects. Chem Sci 2023; 14:5438-5452. [PMID: 37234902 PMCID: PMC10208042 DOI: 10.1039/d2sc04815a] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/03/2023] [Indexed: 07/28/2023] Open
Abstract
Deep-HP is a scalable extension of the Tinker-HP multi-GPU molecular dynamics (MD) package enabling the use of Pytorch/TensorFlow Deep Neural Network (DNN) models. Deep-HP increases DNNs' MD capabilities by orders of magnitude offering access to ns simulations for 100k-atom biosystems while offering the possibility of coupling DNNs to any classical (FFs) and many-body polarizable (PFFs) force fields. It allows therefore the introduction of the ANI-2X/AMOEBA hybrid polarizable potential designed for ligand binding studies where solvent-solvent and solvent-solute interactions are computed with the AMOEBA PFF while solute-solute ones are computed by the ANI-2X DNN. ANI-2X/AMOEBA explicitly includes AMOEBA's physical long-range interactions via an efficient Particle Mesh Ewald implementation while preserving ANI-2X's solute short-range quantum mechanical accuracy. The DNN/PFF partition can be user-defined allowing for hybrid simulations to include key ingredients of biosimulation such as polarizable solvents, polarizable counter ions, etc.… ANI-2X/AMOEBA is accelerated using a multiple-timestep strategy focusing on the model's contributions to low-frequency modes of nuclear forces. It primarily evaluates AMOEBA forces while including ANI-2X ones only via correction-steps resulting in an order of magnitude acceleration over standard Velocity Verlet integration. Simulating more than 10 μs, we compute charged/uncharged ligand solvation free energies in 4 solvents, and absolute binding free energies of host-guest complexes from SAMPL challenges. ANI-2X/AMOEBA average errors are discussed in terms of statistical uncertainty and appear in the range of chemical accuracy compared to experiment. The availability of the Deep-HP computational platform opens the path towards large-scale hybrid DNN simulations, at force-field cost, in biophysics and drug discovery.
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Affiliation(s)
- Théo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Olivier Adjoua
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin Austin Texas USA
| | - Hatice Gökcan
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania USA
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania USA
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique FR 2622 CNRS Paris France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique UMR 7616 CNRS Paris 75005 France
- Department of Biomedical Engineering, University of Texas at Austin Austin Texas USA
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4
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Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
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Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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5
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Nicoli L, Giovannini T, Cappelli C. Assessing the quality of QM/MM approaches to describe vacuo-to-water solvatochromic shifts. J Chem Phys 2022; 157:214101. [PMID: 36511555 DOI: 10.1063/5.0118664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The performance of different quantum mechanics/molecular mechanics embedding models to compute vacuo-to-water solvatochromic shifts is investigated. In particular, both nonpolarizable and polarizable approaches are analyzed and computed results are compared to reference experimental data. We show that none of the approaches outperform the others and that errors strongly depend on the nature of the molecular transition to be described. Thus, we prove that the best choice of embedding model highly depends on the molecular system and that the use of a specific approach as a black box can lead to significant errors and, sometimes, totally wrong predictions.
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Affiliation(s)
- Luca Nicoli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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6
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Salahub DR. Multiscale molecular modelling: from electronic structure to dynamics of nanosystems and beyond. Phys Chem Chem Phys 2022; 24:9051-9081. [PMID: 35389399 DOI: 10.1039/d1cp05928a] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Important contemporary biological and materials problems often depend on interactions that span orders of magnitude differences in spatial and temporal dimensions. This Tutorial Review attempts to provide an introduction to such fascinating problems through a series of case studies, aimed at beginning researchers, graduate students, postdocs and more senior colleagues who are changing direction to focus on multiscale aspects of their research. The choice of specific examples is highly personal, with examples either chosen from our own work or outstanding multiscale efforts from the literature. I start with various embedding schemes, as exemplified by polarizable continuum models, 3-D RISM, molecular DFT and frozen-density embedding. Next, QM/MM (quantum mechanical/molecular mechanical) techniques are the workhorse of pm-to-nm/ps-to-ns simulations; examples are drawn from enzymes and from nanocatalysis for oil-sands upgrading. Using polarizable force-fields in the QM/MM framework represents a burgeoning subfield; with examples from ion channels and electron dynamics in molecules subject to strong external fields, probing the atto-second dynamics of the electrons with RT-TDDFT (real-time - time-dependent density functional theory) eventually coupled with nuclear motion through the Ehrenfest approximation. This is followed by a section on coarse graining, bridging dimensions from atoms to cells. The penultimate chapter gives a quick overview of multiscale approaches that extend into the meso- and macro-scales, building on atomistic and coarse-grained techniques to enter the world of materials engineering, on the one hand, and cell biology, on the other. A final chapter gives just a glimpse of the burgeoning impact of machine learning on the structure-dynamics front. I aim to capture the excitement of contemporary leading-edge breakthroughs in the description of physico-chemical systems and processes in complex environments, with only enough historical content to provide context and aid the next generation of methodological development. While I aim also for a clear description of the essence of methodological breakthroughs, equations are kept to a minimum and detailed formalism and implementation details are left to the references. My approach is very selective (case studies) rather than exhaustive. I think that these case studies should provide fodder to build as complete a reference tree on multiscale modelling as the reader may wish, through forward and backward citation analysis. I hope that my choices of cases will excite interest in newcomers and help to fuel the growth of multiscale modelling in general.
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Affiliation(s)
- Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
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7
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Deng J, Cui Q. Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants. J Am Chem Soc 2022; 144:4594-4610. [PMID: 35239338 PMCID: PMC9616648 DOI: 10.1021/jacs.2c00312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Buried charged residues play important roles in the modulation of protein stabilities and conformational dynamics and make crucial contributions to protein functions. Considering the generally nonpolar nature of protein interior, a key question concerns the contribution of electronic polarization to the stabilization and properties of buried charges. We answer this question by conducting free energy simulations using the latest polarizable CHARMM force field based on Drude oscillators for a series of Staphylococcal nuclease mutants that involve a buried Glu-Lys pair in different titration states and orientations. While a nonpolarizable model suggests that the ionized form of the buried Glu-Lys pair is more than 40 kcal/mol less stable than the charge-neutral form, the two titration states are comparable in stability when electronic polarization is included explicitly, a result better reconcilable with available experimental data. Analysis of free energy components suggests that additional stabilization of the ionized Glu-Lys pair has contributions from both the enhanced salt-bridge strength and stronger interaction between the ion-pair and surrounding protein residues and penetrated water. Despite the stronger direct interaction between Glu and Lys, the ion-pair exhibits considerably larger and faster structural fluctuations when polarization is included, due to compensation of interactions in the cavity. Collectively, observations from this work provide compelling evidence that electronic polarization is essential to the stability, hydration, dynamics, and therefore function of buried charges in proteins. Therefore, our study advocates for the explicit consideration of electronic polarization for mechanistic and engineering studies that implicate buried charged residues, such as enzymes and ion transporters.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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8
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Brandt F, Jacob CR. Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification. J Chem Theory Comput 2022; 18:2584-2596. [PMID: 35271768 DOI: 10.1021/acs.jctc.1c01093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While QM/MM studies of enzymatic reactions are widely used in computational chemistry, the results of such studies are subject to numerous sources of uncertainty, and the effect of different choices by the simulation scientist that are required when setting up QM/MM calculations is often unclear. In particular, the selection of the QM region is crucial for obtaining accurate and reliable results. Simply including amino acids by their distance to the active site is mostly not sufficient as necessary residues are missing or unimportant residues are included without evidence. Here, we take a first step toward quantifying uncertainties in QM/MM calculations by assessing the sensitivity of QM/MM reaction energies with respect to variations of the MM point charges. We show that such a point charge variation analysis (PCVA) can be employed to judge the accuracy of QM/MM reaction energies obtained with a selected QM region and devise a protocol to systematically construct QM regions that minimize this uncertainty. We apply such a PCVA to the example of catechol O-methyltransferase and demonstrate that it provides a simple and reliable approach for the construction of the QM region. Our PCVA-based scheme is computationally efficient and requires only calculations for a system with a minimal QM region. Our work highlights the promise of applying methods of uncertainty quantification in computational chemistry.
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Affiliation(s)
- Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
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9
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Rossano‐Tapia M, Brown A. Quantum mechanical/molecular mechanical studies of photophysical properties of fluorescent proteins. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Alex Brown
- Department of Chemistry University of Alberta Edmonton Alberta Canada
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10
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Kaila VRI. Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I. Acc Chem Res 2021; 54:4462-4473. [PMID: 34894649 PMCID: PMC8697550 DOI: 10.1021/acs.accounts.1c00524] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
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Biological energy conversion is catalyzed by membrane-bound proteins
that transduce chemical or light energy into energy forms that power
endergonic processes in the cell. At a molecular level, these catalytic
processes involve elementary electron-, proton-, charge-, and energy-transfer
reactions that take place in the intricate molecular machineries of
cell respiration and photosynthesis. Recent developments in structural
biology, particularly cryo-electron microscopy (cryoEM), have resolved
the molecular architecture of several energy transducing proteins,
but detailed mechanistic principles of their charge transfer reactions
still remain poorly understood and a major challenge for modern biochemical
research. To this end, multiscale molecular simulations provide a
powerful approach to probe mechanistic principles on a broad range
of time scales (femtoseconds to milliseconds) and spatial resolutions
(101–106 atoms), although technical challenges
also require balancing between the computational accuracy, cost, and
approximations introduced within the model. Here we discuss how the
combination of atomistic (aMD) and hybrid quantum/classical molecular
dynamics (QM/MM MD) simulations with free energy (FE) sampling methods
can be used to probe mechanistic principles of enzymes responsible
for biological energy conversion. We present mechanistic explorations
of long-range proton-coupled electron transfer (PCET) dynamics in
the highly intricate respiratory chain enzyme Complex I, which functions
as a redox-driven proton pump in bacterial and mitochondrial respiratory
chains by catalyzing a 300 Å fully reversible PCET process. This
process is initiated by a hydride (H–) transfer
between NADH and FMN, followed by long-range (>100 Å) electron
transfer along a wire of 8 FeS centers leading to a quinone biding
site. The reduction of the quinone to quinol initiates dissociation
of the latter to a second membrane-bound binding site, and triggers
proton pumping across the membrane domain of complex I, in subunits
up to 200 Å away from the active site. Our simulations across
different size and time scales suggest that transient charge transfer
reactions lead to changes in the internal hydration state of key regions,
local electric fields, and the conformation of conserved ion pairs,
which in turn modulate the dynamics of functional steps along the
reaction cycle. Similar functional principles, which operate on much
shorter length scales, are also found in some unrelated proteins,
suggesting that enzymes may employ conserved principles in the catalysis
of biological energy transduction processes.
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Affiliation(s)
- Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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11
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Ambrosetti M, Skoko S, Giovannini T, Cappelli C. Quantum Mechanics/Fluctuating Charge Protocol to Compute Solvatochromic Shifts. J Chem Theory Comput 2021; 17:7146-7156. [PMID: 34619965 PMCID: PMC8582258 DOI: 10.1021/acs.jctc.1c00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Despite the potentialities
of the quantum mechanics (QM)/fluctuating
charge (FQ) approach to model the spectral properties of solvated
systems, its extensive use has been hampered by the lack of reliable
parametrizations of solvents other than water. In this paper, we substantially
extend the applicability of QM/FQ to solvating environments of different
polarities and hydrogen-bonding capabilities. The reliability and
robustness of the approach are demonstrated by challenging the model
to simulate solvatochromic shifts of four organic chromophores, which
display large shifts when dissolved in apolar, aprotic or polar, protic
solvents.
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Affiliation(s)
| | - Sulejman Skoko
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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12
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Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Phys Chem Chem Phys 2021; 23:22227-22240. [PMID: 34586107 PMCID: PMC8516722 DOI: 10.1039/d1cp03800a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
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