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Aldossary A, Campos-Gonzalez-Angulo JA, Pablo-García S, Leong SX, Rajaonson EM, Thiede L, Tom G, Wang A, Avagliano D, Aspuru-Guzik A. In Silico Chemical Experiments in the Age of AI: From Quantum Chemistry to Machine Learning and Back. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2402369. [PMID: 38794859 DOI: 10.1002/adma.202402369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/28/2024] [Indexed: 05/26/2024]
Abstract
Computational chemistry is an indispensable tool for understanding molecules and predicting chemical properties. However, traditional computational methods face significant challenges due to the difficulty of solving the Schrödinger equations and the increasing computational cost with the size of the molecular system. In response, there has been a surge of interest in leveraging artificial intelligence (AI) and machine learning (ML) techniques to in silico experiments. Integrating AI and ML into computational chemistry increases the scalability and speed of the exploration of chemical space. However, challenges remain, particularly regarding the reproducibility and transferability of ML models. This review highlights the evolution of ML in learning from, complementing, or replacing traditional computational chemistry for energy and property predictions. Starting from models trained entirely on numerical data, a journey set forth toward the ideal model incorporating or learning the physical laws of quantum mechanics. This paper also reviews existing computational methods and ML models and their intertwining, outlines a roadmap for future research, and identifies areas for improvement and innovation. Ultimately, the goal is to develop AI architectures capable of predicting accurate and transferable solutions to the Schrödinger equation, thereby revolutionizing in silico experiments within chemistry and materials science.
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Affiliation(s)
- Abdulrahman Aldossary
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | | | - Sergio Pablo-García
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
- Department of Computer Science, University of Toronto, 40 St. George Street, Toronto, ON, M5S 2E4, Canada
| | - Shi Xuan Leong
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Ella Miray Rajaonson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
- Vector Institute for Artificial Intelligence, 661 University Ave. Suite 710, Toronto, ON, M5G 1M1, Canada
| | - Luca Thiede
- Department of Computer Science, University of Toronto, 40 St. George Street, Toronto, ON, M5S 2E4, Canada
- Vector Institute for Artificial Intelligence, 661 University Ave. Suite 710, Toronto, ON, M5G 1M1, Canada
| | - Gary Tom
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
- Vector Institute for Artificial Intelligence, 661 University Ave. Suite 710, Toronto, ON, M5G 1M1, Canada
| | - Andrew Wang
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Davide Avagliano
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (iCLeHS UMR 8060), Paris, F-75005, France
| | - Alán Aspuru-Guzik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
- Department of Computer Science, University of Toronto, 40 St. George Street, Toronto, ON, M5S 2E4, Canada
- Vector Institute for Artificial Intelligence, 661 University Ave. Suite 710, Toronto, ON, M5G 1M1, Canada
- Department of Materials Science & Engineering, University of Toronto, 184 College St., Toronto, ON, M5S 3E4, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College St., Toronto, ON, M5S 3E5, Canada
- Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR), 66118 University Ave., Toronto, M5G 1M1, Canada
- Acceleration Consortium, 80 St George St, Toronto, M5S 3H6, Canada
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2
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Silvestri I, Manigrasso J, Andreani A, Brindani N, Mas C, Reiser JB, Vidossich P, Martino G, McCarthy AA, De Vivo M, Marcia M. Targeting the conserved active site of splicing machines with specific and selective small molecule modulators. Nat Commun 2024; 15:4980. [PMID: 38898052 PMCID: PMC11187226 DOI: 10.1038/s41467-024-48697-0] [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] [Received: 06/21/2023] [Accepted: 05/06/2024] [Indexed: 06/21/2024] Open
Abstract
The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.
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Affiliation(s)
- Ilaria Silvestri
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
- Institute of Crystallography, National Research Council, Via Vivaldi 43, 81100, Caserta, Italy
| | - Jacopo Manigrasso
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alessandro Andreani
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Nicoletta Brindani
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Caroline Mas
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, ISBG, F-38000, Grenoble, France
| | | | - Pietro Vidossich
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Gianfranco Martino
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Andrew A McCarthy
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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3
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Liu J, Ma H, Shang H, Li Z, Yang J. Quantum-centric high performance computing for quantum chemistry. Phys Chem Chem Phys 2024; 26:15831-15843. [PMID: 38787657 DOI: 10.1039/d4cp00436a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
High performance computing (HPC) is renowned for its capacity to tackle complex problems. Meanwhile, quantum computing (QC) provides a potential way to accurately and efficiently solve quantum chemistry problems. The emerging field of quantum-centric high performance computing (QCHPC), which merges these two powerful technologies, is anticipated to enhance computational capabilities for solving challenging problems in quantum chemistry. The implementation of QCHPC for quantum chemistry requires interdisciplinary research and collaboration across multiple fields, including quantum chemistry, quantum physics, computer science and so on. This perspective provides an introduction to the quantum algorithms that are suitable for deployment in QCHPC, focusing on conceptual insights rather than technical details. Parallel strategies to implement these algorithms on quantum-centric supercomputers are discussed. We also summarize high performance quantum emulating simulators, which are considered a viable tool to explore QCHPC. We conclude with challenges and outlooks in this field.
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Affiliation(s)
- Jie Liu
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
| | - Huan Ma
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
| | - Honghui Shang
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhenyu Li
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Jinlong Yang
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
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4
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Asgharpour S, Chi LA, Spehr M, Carloni P, Alfonso-Prieto M. Fluoride Transport and Inhibition Across CLC Transporters. Handb Exp Pharmacol 2024; 283:81-100. [PMID: 36042142 DOI: 10.1007/164_2022_593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Chloride Channel (CLC) family includes proton-coupled chloride and fluoride transporters. Despite their similar protein architecture, the former exchange two chloride ions for each proton and are inhibited by fluoride, whereas the latter efficiently transport one fluoride in exchange for one proton. The combination of structural, mutagenesis, and functional experiments with molecular simulations has pinpointed several amino acid changes in the permeation pathway that capitalize on the different chemical properties of chloride and fluoride to fine-tune protein function. Here we summarize recent findings on fluoride inhibition and transport in the two prototypical members of the CLC family, the chloride/proton transporter from Escherichia coli (CLC-ec1) and the fluoride/proton transporter from Enterococcus casseliflavus (CLCF-eca).
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Affiliation(s)
- Somayeh Asgharpour
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - L América Chi
- Laboratory for the Design and Development of New Drugs and Biotechnological Innovation, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México, Mexico
| | - Marc Spehr
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Paolo Carloni
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany.
- Department of Physics, RWTH Aachen University, Aachen, Germany.
- JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Jülich, Germany.
- JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.
- Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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5
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Laurent H, Hughes MDG, Walko M, Brockwell DJ, Mahmoudi N, Youngs TGA, Headen TF, Dougan L. Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering. Biomacromolecules 2023; 24:4869-4879. [PMID: 37874935 PMCID: PMC10646990 DOI: 10.1021/acs.biomac.3c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/03/2023] [Indexed: 10/26/2023]
Abstract
Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled β hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model β hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.
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Affiliation(s)
- Harrison Laurent
- School
of Physics and Astronomy, University of
Leeds, Leeds, United Kingdom, LS2
9JT
| | - Matt D. G. Hughes
- School
of Physics and Astronomy, University of
Leeds, Leeds, United Kingdom, LS2
9JT
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom LS2
9JT
| | - Martin Walko
- School
of Chemistry, University of Leeds, Leeds, United
Kingdom, LS2 9JT
| | - David J. Brockwell
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom LS2
9JT
| | - Najet Mahmoudi
- ISIS
Neutron and Muon Source, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, United Kingdom, OX11 0QX
| | - Tristan G. A. Youngs
- ISIS
Neutron and Muon Source, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, United Kingdom, OX11 0QX
| | - Thomas F. Headen
- ISIS
Neutron and Muon Source, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, United Kingdom, OX11 0QX
| | - Lorna Dougan
- School
of Physics and Astronomy, University of
Leeds, Leeds, United Kingdom, LS2
9JT
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom LS2
9JT
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6
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Clemente CM, Capece L, Martí MA. Best Practices on QM/MM Simulations of Biological Systems. J Chem Inf Model 2023; 63:2609-2627. [PMID: 37100031 DOI: 10.1021/acs.jcim.2c01522] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
During the second half of the 20th century, following structural biology hallmark works on DNA and proteins, biochemists shifted their questions from "what does this molecule look like?" to "how does this process work?". Prompted by the theoretical and practical developments in computational chemistry, this led to the emergence of biomolecular simulations and, along with the 2013 Nobel Prize in Chemistry, to the development of hybrid QM/MM methods. QM/MM methods are necessary whenever the problem we want to address involves chemical reactivity and/or a change in the system's electronic structure, with archetypal examples being the studies of an enzyme's reaction mechanism and a metalloprotein's active site. In the last decades QM/MM methods have seen an increasing adoption driven by their incorporation in widely used biomolecular simulation software. However, properly setting up a QM/MM simulation is not an easy task, and several issues need to be properly addressed to obtain meaningful results. In the present work, we describe both the theoretical concepts and practical issues that need to be considered when performing QM/MM simulations. We start with a brief historical perspective on the development of these methods and describe when and why QM/MM methods are mandatory. Then we show how to properly select and analyze the performance of the QM level of theory, the QM system size, and the position and type of the boundaries. We show the relevance of performing prior QM model system (or QM cluster) calculations in a vacuum and how to use the corresponding results to adequately calibrate those derived from QM/MM. We also discuss how to prepare the starting structure and how to select an adequate simulation strategy, including those based on geometry optimizations as well as free energy methods. In particular, we focus on the determination of free energy profiles using multiple steered molecular dynamics (MSMD) combined with Jarzynski's equation. Finally, we describe the results for two illustrative and complementary examples: the reaction performed by chorismate mutase and the study of ligand binding to hemoglobins. Overall, we provide many practical recommendations (or shortcuts) together with important conceptualizations that we hope will encourage more and more researchers to incorporate QM/MM studies into their research projects.
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Affiliation(s)
- Camila M Clemente
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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7
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Church JR, Olsen JMH, Schapiro I. Induction effects on the absorption maxima of photoreceptor proteins. Biophys Physicobiol 2023; 20:e201007. [PMID: 38362325 PMCID: PMC10865876 DOI: 10.2142/biophysico.bppb-v20.s007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Multiscale simulations have been established as a powerful tool to calculate and predict excitation energies in complex systems such as photoreceptor proteins. In these simulations the chromophore is typically treated using quantum mechanical (QM) methods while the protein and surrounding environment are described by a classical molecular mechanics (MM) force field. The electrostatic interactions between these regions are often treated using electrostatic embedding where the point charges in the MM region polarize the QM region. A more sophisticated treatment accounts also for the polarization of the MM region. In this work, the effect of such a polarizable embedding on excitation energies was benchmarked and compared to electrostatic embedding. This was done for two different proteins, the lipid membrane-embedded jumping spider rhodopsin and the soluble cyanobacteriochrome Slr1393g3. It was found that the polarizable embedding scheme produces absorption maxima closer to experimental values. The polarizable embedding scheme was also benchmarked against expanded QM regions and found to be in qualitative agreement. Treating individual residues as polarizable recovered between 50% and 71% of the QM improvement in the excitation energies, depending on the system. A detailed analysis of each amino acid residue in the chromophore binding pocket revealed that aromatic residues result in the largest change in excitation energy compared to the electrostatic embedding. Furthermore, the computational efficiency of polarizable embedding allowed it to go beyond the binding pocket and describe a larger portion of the environment, further improving the results.
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Affiliation(s)
- Jonathan R. Church
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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8
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Henderson JM, Podzorova M, Cerezo M, Golden JK, Gleyzer L, Viswanathan HS, O’Malley D. Quantum algorithms for geologic fracture networks. Sci Rep 2023; 13:2906. [PMID: 36805641 PMCID: PMC9938886 DOI: 10.1038/s41598-023-29643-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/08/2023] [Indexed: 02/20/2023] Open
Abstract
Solving large systems of equations is a challenge for modeling natural phenomena, such as simulating subsurface flow. To avoid systems that are intractable on current computers, it is often necessary to neglect information at small scales, an approach known as coarse-graining. For many practical applications, such as flow in porous, homogenous materials, coarse-graining offers a sufficiently-accurate approximation of the solution. Unfortunately, fractured systems cannot be accurately coarse-grained, as critical network topology exists at the smallest scales, including topology that can push the network across a percolation threshold. Therefore, new techniques are necessary to accurately model important fracture systems. Quantum algorithms for solving linear systems offer a theoretically-exponential improvement over their classical counterparts, and in this work we introduce two quantum algorithms for fractured flow. The first algorithm, designed for future quantum computers which operate without error, has enormous potential, but we demonstrate that current hardware is too noisy for adequate performance. The second algorithm, designed to be noise resilient, already performs well for problems of small to medium size (order 10-1000 nodes), which we demonstrate experimentally and explain theoretically. We expect further improvements by leveraging quantum error mitigation and preconditioning.
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Affiliation(s)
- Jessie M. Henderson
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM 87545 USA ,grid.263864.d0000 0004 1936 7929Southern Methodist University, Dallas, TX 75205 USA
| | - Marianna Podzorova
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM 87545 USA ,grid.148313.c0000 0004 0428 3079Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA ,grid.410443.60000 0004 0370 3414Department of Computer Science and Joint Center for Quantum Information and Computer Science, The University of Maryland, College Park, MD, 20742 USA
| | - M. Cerezo
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM 87545 USA ,grid.148313.c0000 0004 0428 3079Information Sciences, Los Alamos National Laboratory, Los Alamos, NM 87545 USA ,grid.148313.c0000 0004 0428 3079Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544 USA
| | - John K. Golden
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM 87545 USA ,grid.148313.c0000 0004 0428 3079Information Sciences, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Leonard Gleyzer
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM 87545 USA ,grid.40263.330000 0004 1936 9094Brown University, Providence, RI 02912 USA
| | - Hari S. Viswanathan
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Daniel O’Malley
- grid.148313.c0000 0004 0428 3079Los Alamos National Laboratory, Los Alamos, NM 87545 USA
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9
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Gentili D, Ori G. Reversible assembly of nanoparticles: theory, strategies and computational simulations. NANOSCALE 2022; 14:14385-14432. [PMID: 36169572 DOI: 10.1039/d2nr02640f] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The significant advances in synthesis and functionalization have enabled the preparation of high-quality nanoparticles that have found a plethora of successful applications. The unique physicochemical properties of nanoparticles can be manipulated through the control of size, shape, composition, and surface chemistry, but their technological application possibilities can be further expanded by exploiting the properties that emerge from their assembly. The ability to control the assembly of nanoparticles not only is required for many real technological applications, but allows the combination of the intrinsic properties of nanoparticles and opens the way to the exploitation of their complex interplay, giving access to collective properties. Significant advances and knowledge gained over the past few decades on nanoparticle assembly have made it possible to implement a growing number of strategies for reversible assembly of nanoparticles. In addition to being of interest for basic studies, such advances further broaden the range of applications and the possibility of developing innovative devices using nanoparticles. This review focuses on the reversible assembly of nanoparticles and includes the theoretical aspects related to the concept of reversibility, an up-to-date assessment of the experimental approaches applied to this field and the advanced computational schemes that offer key insights into the assembly mechanisms. We aim to provide readers with a comprehensive guide to address the challenges in assembling reversible nanoparticles and promote their applications.
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Affiliation(s)
- Denis Gentili
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Via P. Gobetti 101, 40129 Bologna, Italy.
| | - Guido Ori
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Rue du Loess 23, F-67034 Strasbourg, France.
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10
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Reisjalali M, Manurung R, Carbone P, Troisi A. Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2022; 7:294-305. [PMID: 35646391 PMCID: PMC9074845 DOI: 10.1039/d1me00165e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/06/2022] [Indexed: 05/05/2023]
Abstract
Decades of work in the field of computational study of semiconducting polymers using atomistic models illustrate the challenges of generating equilibrated models for this class of materials. While adopting a coarse-grained model can be helpful, the process of developing a suitable model is particularly non-trivial and time-consuming for semiconducting polymers due to a large number of different interactions with some having an anisotropic nature. This work introduces a procedure for the rapid generation of a hybrid model for semiconducting polymers where atoms of secondary importance (those in the alkyl side chains) are transformed into coarse-grained beads to reduce the computational cost of generating an equilibrated structure. The parameters are determined from easy-to-equilibrate simulations of very short oligomers and the model is constructed to enable a very simple back-mapping procedure to reconstruct geometries with atomistic resolution. The model is illustrated for three related polymers containing DPP (diketopyrrolopyrrole) to evaluate the transferability of the potential across different families of polymers. The accuracy of the model, determined by comparison with the results of fully equilibrated simulations of the same material before and after back-mapping, is fully satisfactory for two out of the three cases considered. We noticed that accuracy can be determined very early in the workflow so that it is easy to assess when the deployment of this method is advantageous. The hybrid representation can be used to evaluate directly the electronic properties of structures sampled by the simulations.
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Affiliation(s)
- Maryam Reisjalali
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
| | - Rex Manurung
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
| | - Paola Carbone
- Department of Chemical Engineering and Analytical Science Oxford Road M13 9PL Manchester UK
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
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11
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Enzyme self-aggregation in supramolecular self-assembly of glucose oxidase and catalase: Insight from molecular dynamics simulation based on coarse-grained method. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Soto-Ospina A, Araque Marín P, Bedoya GDJ, Villegas Lanau A. Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. Biochem Res Int 2021; 2021:9542038. [PMID: 34881055 PMCID: PMC8648483 DOI: 10.1155/2021/9542038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease manifests itself in brain tissue by neuronal death, due to aggregation of β-amyloid, produced by senile plaques, and hyperphosphorylation of the tau protein, which produces neurofibrillary tangles. One of the genetic markers of the disease is the gene that translates the presenilin-2 protein, which has mutations that favor the appearance of the disease and has no reported crystallographic structure. In view of this, protein modeling is performed using prediction and structural refinement tools followed by an energetic and stereochemical characterization for its validation. For the simulation, four reported mutations are chosen, which are Met239Ile, Met239Val, Ser130Leu, and Thr122Arg, all associated with various functional responses. From a theoretical analysis, a preliminary bioinformatic study is made to find the phosphorylation patterns in the protein and the hydropathic index according to the polarity and chemical environment. Molecular visualization was carried out with the Chimera 1.14 software, and the theoretical calculation with the hybrid quantum mechanics/molecular mechanics system from the semi-empirical method, with Spartan18 software and an AustinModel1 basis. These relationships allow for studying the system from a structural approach with the determination of small distance changes, potential surfaces, electrostatic maps, and angle changes, which favor the comparison between wild-type and mutant systems. With the results obtained, it is expected to complement experimental data reported in the literature from models that would allow us to understand the effects of the selected mutations.
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Affiliation(s)
- Alejandro Soto-Ospina
- University of Antioquia, Faculty of Medicine, Group Molecular Genetics, Medellín, Colombia
- University of Antioquia, Faculty of Medicine, Group Neuroscience of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- EIA University, School of Life Sciences, Research and Innovation in Chemistry Formulations Group, Envigado, Colombia
| | | | - Andrés Villegas Lanau
- University of Antioquia, Faculty of Medicine, Group Molecular Genetics, Medellín, Colombia
- University of Antioquia, Faculty of Medicine, Group Neuroscience of Antioquia, Medellín, Colombia
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13
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Abstract
Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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14
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Styles KM, Brown AT, Sagona AP. A Review of Using Mathematical Modeling to Improve Our Understanding of Bacteriophage, Bacteria, and Eukaryotic Interactions. Front Microbiol 2021; 12:724767. [PMID: 34621252 PMCID: PMC8490754 DOI: 10.3389/fmicb.2021.724767] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/27/2021] [Indexed: 12/27/2022] Open
Abstract
Phage therapy, the therapeutic usage of viruses to treat bacterial infections, has many theoretical benefits in the ‘post antibiotic era.’ Nevertheless, there are currently no approved mainstream phage therapies. One reason for this is a lack of understanding of the complex interactions between bacteriophage, bacteria and eukaryotic hosts. These three-component interactions are complex, with non-linear or synergistic relationships, anatomical barriers and genetic or phenotypic heterogeneity all leading to disparity between performance and efficacy in in vivo versus in vitro environments. Realistic computer or mathematical models of these complex environments are a potential route to improve the predictive power of in vitro studies for the in vivo environment, and to streamline lab work. Here, we introduce and review the current status of mathematical modeling and highlight that data on genetic heterogeneity and mutational stochasticity, time delays and population densities could be critical in the development of realistic phage therapy models in the future. With this in mind, we aim to inform and encourage the collaboration and sharing of knowledge and expertise between microbiologists and theoretical modelers, synergising skills and smoothing the road to regulatory approval and widespread use of phage therapy.
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Affiliation(s)
- Kathryn M Styles
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Aidan T Brown
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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15
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Koehl P, Orland H, Delarue M. Parameterizing elastic network models to capture the dynamics of proteins. J Comput Chem 2021; 42:1643-1661. [PMID: 34117647 DOI: 10.1002/jcc.26701] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/14/2020] [Accepted: 05/23/2021] [Indexed: 11/09/2022]
Abstract
Coarse-grained normal mode analyses of protein dynamics rely on the idea that the geometry of a protein structure contains enough information for computing its fluctuations around its equilibrium conformation. This geometry is captured in the form of an elastic network (EN), namely a network of edges between its residues. The normal modes of a protein are then identified with the normal modes of its EN. Different approaches have been proposed to construct ENs, focusing on the choice of the edges that they are comprised of, and on their parameterizations by the force constants associated with those edges. Here we propose new tools to guide choices on these two facets of EN. We study first different geometric models for ENs. We compare cutoff-based ENs, whose edges have lengths that are smaller than a cutoff distance, with Delaunay-based ENs and find that the latter provide better representations of the geometry of protein structures. We then derive an analytical method for the parameterization of the EN such that its dynamics leads to atomic fluctuations that agree with experimental B-factors. To limit overfitting, we attach a parameter referred to as flexibility constant to each atom instead of to each edge in the EN. The parameterization is expressed as a non-linear optimization problem whose parameters describe both rigid-body and internal motions. We show that this parameterization leads to improved ENs, whose dynamics mimic MD simulations better than ENs with uniform force constants, and reduces the number of normal modes needed to reproduce functional conformational changes.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Sciences and Genome Center, University of California, Davis, California, USA
| | - Henri Orland
- Institut de Physique Théorique, Université Paris-Saclay, Gif sur Yvette, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, Paris, France
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16
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Barone V, Puzzarini C, Mancini G. Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy. Phys Chem Chem Phys 2021; 23:17079-17096. [PMID: 34346437 DOI: 10.1039/d1cp02507d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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17
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Macetti G, Genoni A. Three-Layer Multiscale Approach Based on Extremely Localized Molecular Orbitals to Investigate Enzyme Reactions. J Phys Chem A 2021; 125:6013-6027. [PMID: 34190569 DOI: 10.1021/acs.jpca.1c05040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) calculations are widely used embedding techniques to computationally investigate enzyme reactions. In most QM/MM computations, the quantum mechanical region is treated through density functional theory (DFT), which offers the best compromise between chemical accuracy and computational cost. Nevertheless, to obtain more accurate results, one should resort to wave function-based methods, which however lead to a much larger computational cost already for relatively small QM subsystems. To overcome this drawback, we propose the coupling of our QM/ELMO (quantum mechanics/extremely localized molecular orbital) approach with molecular mechanics, thus introducing the three-layer QM/ELMO/MM technique. The QM/ELMO strategy is an embedding method in which the chemically relevant part of the system is treated at the quantum mechanical level, while the rest is described through frozen ELMOs. Since the QM/ELMO method reproduces results of fully QM computations within chemical accuracy and with a much lower computational effort, it can be considered a suitable strategy to extend the range of applicability and accuracy of the QM/MM scheme. In this paper, other than briefly presenting the theoretical bases of the QM/ELMO/MM technique, we will also discuss its validation on the well-tested deprotonation of acetyl coenzyme A by aspartate in citrate synthase.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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18
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Soto-Ospina A, Araque Marín P, Bedoya G, Sepulveda-Falla D, Villegas Lanau A. Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer's Disease on the Orthosteric Site. Front Mol Biosci 2021; 8:649990. [PMID: 34150846 PMCID: PMC8206637 DOI: 10.3389/fmolb.2021.649990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease pathology is characterized by β-amyloid plaques and neurofibrillary tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the production of β-amyloid peptides with a length ranging from 38 to 43 amino acids. Presenilin 1 (PS1) is the catalytic unit of γ-secretase, and more than 200 PS1 pathogenic mutations have been identified as causative for Alzheimer's disease. A complete monocrystal structure of PS1 has not been determined so far due to the presence of two flexible domains. We have developed a complete structural model of PS1 using a computational approach with structure prediction software. Missing fragments Met1-Glut72 and Ser290-Glu375 were modeled and validated by their energetic and stereochemical characteristics. Then, with the complete structure of PS1, we defined that these fragments do not have a direct effect in the structure of the pore. Next, we used our hypothetical model for the analysis of the functional effects of PS1 mutations Ala246GLu, Leu248Pro, Leu248Arg, Leu250Val, Tyr256Ser, Ala260Val, and Val261Phe, localized in the catalytic pore. For this, we used a quantum mechanics/molecular mechanics (QM/MM) hybrid method, evaluating modifications in the topology, potential surface density, and electrostatic potential map of mutated PS1 proteins. We found that each mutation exerts changes resulting in structural modifications of the active site and in the shape of the pore. We suggest this as a valid approach for functional studies of PS1 in view of the possible impact in substrate processing and for the design of targeted therapeutic strategies.
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Affiliation(s)
- Alejandro Soto-Ospina
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- School of Life Sciences, Research and Innovation in Chemistry Formulations Group, EIA University, Envigado, Colombia
| | - Gabriel Bedoya
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrés Villegas Lanau
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
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19
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Kantardjiev A. Coarse-grained simulation of the self-assembly of lipid vesicles concomitantly with novel block copolymers with multiple tails. SOFT MATTER 2021; 17:2753-2764. [PMID: 33533781 DOI: 10.1039/d0sm01898h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We carried out a series of coarse-grained molecular dynamics liposome-copolymer simulations with varying extent of copolymer concentration in an attempt to understand the effect of copolymer structure and concentration on vesicle self-assembly and stability. For one particular case molecular dynamics simulation data was successfully verified against experimental NMR results enhancing the credulity in the simulation methodology. The study focused on a new class of promising copolymers based on ethylene oxide (EO) chains and short blocks of aliphatic double chains that mimic lipid tails. The lipid mimetic units are based on 1,3-didodecyloxy-2-glycidylglycerol (DDGG) and 1,3-didodecyloxy-propane-2-ol (DDP). The conducted simulations indicate that multiple lipid anchor-bearing copolymers lead to stable hybrid liposome formations. Single lipid bearing might incur liposome-stabilizing potential for relatively small ethylene oxide chains but fails dramatically in combination with a longer EO-based moiety. The consistency of the theoretical evidence with experimental NMR observation for certain cases provides confidence for the relevance of the methodology in eliciting the factors governing liposome-polymer stability which is of fundamental and practical significance.
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Affiliation(s)
- Alexander Kantardjiev
- Nuclear Magnetic Resonance Center, Institute of Organic Chemistry, Bulgarian Academy of Sciences, ulica Acad. G. Bonchev, blok 9, 1113 Sofia, Bulgaria.
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20
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Macetti G, Wieduwilt EK, Genoni A. QM/ELMO: A Multi-Purpose Fully Quantum Mechanical Embedding Scheme Based on Extremely Localized Molecular Orbitals. J Phys Chem A 2021; 125:2709-2726. [DOI: 10.1021/acs.jpca.0c11450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Erna K. Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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21
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Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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22
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Sokhan VP, Todorov IT. Dissipative particle dynamics: dissipative forces from atomistic simulation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2019.1578353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Vlad P. Sokhan
- STFC Daresbury Laboratory, Sci-Tech Daresbury, Cheshire, UK
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23
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Nakliang P, Yoon S, Choi S. Emerging computational approaches for the study of regio- and stereoselectivity in organic synthesis. Org Chem Front 2021. [DOI: 10.1039/d1qo00531f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Computational chemistry has become important in organic synthesis as it provides a detailed understanding of molecular structures and properties and detailed reaction mechanisms.
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Affiliation(s)
- Pratanphorn Nakliang
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sanghee Yoon
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China
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24
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Quantum mechanics/extremely localized molecular orbital embedding technique: Theoretical foundations and further validation. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Multiscale mechanisms of reaction-diffusion process in electrode systems: A classical density functional study. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Souza FR, Souza LMP, Pimentel AS. Recent Open Issues in Coarse Grained Force Fields. J Chem Inf Model 2020; 60:5881-5884. [PMID: 33231448 DOI: 10.1021/acs.jcim.0c01265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This viewpoint intends to show recent open issues of using coarse grained models in molecular dynamics simulation. It reviews the current knowledge of the comparison between experimental and simulation data of structural and physical chemical properties that depend on the hydrophilic and hydrophobic behavior of the molecule.
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Affiliation(s)
- Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
| | - Lucas Miguel Pereira Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
| | - Andre Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
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27
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Mancini G, Del Galdo S, Chandramouli B, Pagliai M, Barone V. Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics. J Chem Theory Comput 2020; 16:5747-5761. [PMID: 32697580 PMCID: PMC8009517 DOI: 10.1021/acs.jctc.0c00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Multiscale QM/MM approaches have
become the most suitable and effective
methods for the investigation of spectroscopic properties of medium-
or large-size chromophores in condensed phases. On these grounds,
we are developing a novel workflow aimed at improving the generality,
reliability, and ease of use of the available tools. In the present
paper, we report the latest developments of such an approach with
specific reference to a general workplan starting with the addition
of acetonitrile to the panel of solvents already available in the
General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic
boundary conditions (NPBC). Next, the solvatochromic shifts induced
by acetonitrile on both rigid (uracil and thymine) and flexible (thyrosine)
chromophores have been studied introducing in our software a number
of new features ranging from rigid-geometry NPBC molecular dynamics
based on the quaternion formalism to a full integration of variational
(ONIOM) and perturbative (perturbed matrix method (PMM)) approaches
for describing different solute–solvent topologies and local
fluctuations, respectively. Finally, thymine and uracil have been
studied also in methanol to point out the generality of the computational
strategy. While further developments are surely needed, the strengths
of our integrated approach even in its present version are demonstrated
by the accuracy of the results obtained by an unsupervised approach
and coupled to a computational cost strongly reduced with respect
to that of conventional QM/MM models without any appreciable accuracy
deterioration.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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Puzzarini C, Spada L, Alessandrini S, Barone V. The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:343002. [PMID: 32203942 DOI: 10.1088/1361-648x/ab8253] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/23/2020] [Indexed: 06/10/2023]
Abstract
In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
| | - Lorenzo Spada
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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Del Galdo S, Fusè M, Barone V. The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study. J Chem Theory Comput 2020; 16:3294-3306. [PMID: 32250614 PMCID: PMC7222099 DOI: 10.1021/acs.jctc.0c00124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
This paper deals
with the development and first validation of a
composite approach for the simulation of chiroptical spectra in solution
aimed to strongly reduce the number of full QM computations without
any significant accuracy loss. The approach starts from the quantum
mechanical computation of reference spectra including vibrational
averaging effects and taking average solvent effects into account
by means of the polarizable continuum model. Next, the snapshots of
classical molecular dynamics computations are clusterized and one
reference configuration from each cluster is used to compute a reference
spectrum. Local fluctuation effects within each cluster are then taken
into account by means of the perturbed matrix model. The performance
of the proposed approach is tested on the challenging case of the
optical and chiroptical spectra
of camphorquinone in methanol solution. Although further validations
are surely needed, the results of this first study are quite promising
also taking into account that agreement with experimental data is
reached by just a couple of full quantum mechanical geometry optimizations
and frequency computations.
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Affiliation(s)
- Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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31
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Chizallet C. Toward the Atomic Scale Simulation of Intricate Acidic Aluminosilicate Catalysts. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01136] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Céline Chizallet
- IFP Energies nouvelles Solaize, Rond-Point de l’Echangeur de Solaize, BP 3, 69360 Solaize, France
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32
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Zhai Y, Caruso A, Gao S, Paesani F. Active learning of many-body configuration space: Application to the Cs+–water MB-nrg potential energy function as a case study. J Chem Phys 2020; 152:144103. [DOI: 10.1063/5.0002162] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Yaoguang Zhai
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Alessandro Caruso
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Sicun Gao
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
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33
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Topological Dynamics of a Radical Ion Pair: Experimental and Computational Assessment at the Relevant Nanosecond Timescale. CHEMISTRY 2020. [DOI: 10.3390/chemistry2020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chemical processes mostly happen in fluid environments where reaction partners encounter via diffusion. The bimolecular encounters take place at a nanosecond time scale. The chemical environment (e.g., solvent molecules, (counter)ions) has a decisive influence on the reactivity as it determines the contact time between two molecules and affects the energetics. For understanding reactivity at an atomic level and at the appropriate dynamic time scale, it is crucial to combine matching experimental and theoretical data. Here, we have utilized all-atom molecular-dynamics simulations for accessing the key time scale (nanoseconds) using a QM/MM-Hamiltonian. Ion pairs consisting of a radical ion and its counterion are ideal systems to assess the theoretical predictions because they reflect dynamics at an appropriate time scale when studied by temperature-dependent EPR spectroscopy. We have investigated a diketone radical anion with its tetra-ethylammonium counterion. We have established a funnel-like transition path connecting two (equivalent) complexation sites. The agreement between the molecular-dynamics simulation and the experimental data presents a new paradigm for ion–ion interactions. This study exemplarily demonstrates the impact of the molecular environment on the topological states of reaction intermediates and how these states can be consistently elucidated through the combination of theory and experiment. We anticipate that our findings will contribute to the prediction of bimolecular transformations in the condensed phase with relevance to chemical synthesis, polymers, and biological activity.
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de Souza RM, Ratochinski RH, Karttunen M, Dias LG. Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles. J Chem Inf Model 2020; 60:522-536. [PMID: 31714768 DOI: 10.1021/acs.jcim.9b00790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ELBA coarse-grained force field was originally developed for lipids, and its water model is described as a single-site Lennard-Jones particle with electrostatics modeled by an embedded point-dipole, while other molecules in this force field have a three (or four)-to-one mapping scheme. Here, ELBA was applied to investigate the self-assembly processes of dodecyl-phosphocholine (DPC) micelle, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dihexaoyl-sn-glycero-3-phosphocholine (DPPC/DHPC) bicelles, and DPPC/cyclohexane/water reverse micelles through coarse-grained molecular dynamics (MD) simulations. New parameters were obtained using a simplex algorithm-based calibration procedure to determine the Lennard-Jones parameters for cyclohexane, dodecane, and cyclohexane-dodecane cross-interactions. Density, self-diffusion coefficient, surface tension, and mixture excess volume were found to be in fair agreement with experimental data. These new parameters were used in the simulations, and the obtained structures were analyzed for shape, size, volume, and surface area. Except for the shape of DPC micelles, all other properties match well with available experimental data and all-atom simulations. Remarkably, in agreement with experiments the rodlike shape of the DPPC reverse micelle is well described by ELBA, while all-atom data in the literature predicts a disclike shape. To further check the consistency of the force field in reproducing the correct shapes of reverse micelles, additional simulations were performed doubling the system size. Two distinct reverse micelles were obtained both presenting the rodlike shape and correct aggregation number.
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Affiliation(s)
- R M de Souza
- Department of Chemistry , The University of Western Ontario , London , Ontario , Canada N6A 3K7.,Departamento de Química, FFCLRP , Universidade de São Paulo , Avenida Bandeirantes 3900 , 14040-901 Ribeirão Preto , SP , Brazil.,The Center for Advanced Materials and Biomaterials Research , The University of Western Ontario , London , Ontario , Canada N6K 3K7
| | - R H Ratochinski
- Departamento de Química, FFCLRP , Universidade de São Paulo , Avenida Bandeirantes 3900 , 14040-901 Ribeirão Preto , SP , Brazil
| | - Mikko Karttunen
- Department of Chemistry , The University of Western Ontario , London , Ontario , Canada N6A 3K7.,The Center for Advanced Materials and Biomaterials Research , The University of Western Ontario , London , Ontario , Canada N6K 3K7.,Department of Applied Mathematics , The University of Western Ontario , London , Ontario , Canada N6A 5B7
| | - L G Dias
- Departamento de Química, FFCLRP , Universidade de São Paulo , Avenida Bandeirantes 3900 , 14040-901 Ribeirão Preto , SP , Brazil
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35
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Liu Y, Liu H. Development of reaction–diffusion DFT and its application to catalytic oxidation of NO in porous materials. AIChE J 2019. [DOI: 10.1002/aic.16824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yu Liu
- School of Chemical Engineering and Technology Sun Yat‐sen University Zhuhai China
| | - Honglai Liu
- State Key Laboratory of Chemical Engineering and School of Chemistry & Molecular Engineering East China University of Science and Technology Shanghai China
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36
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Hildebrand PW, Rose AS, Tiemann JK. Bringing Molecular Dynamics Simulation Data into View. Trends Biochem Sci 2019; 44:902-913. [DOI: 10.1016/j.tibs.2019.06.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 12/14/2022]
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Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications. Int J Mol Sci 2019; 20:ijms20153774. [PMID: 31375023 PMCID: PMC6696403 DOI: 10.3390/ijms20153774] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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39
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Ranaghan KE, Shchepanovska D, Bennie SJ, Lawan N, Macrae SJ, Zurek J, Manby FR, Mulholland AJ. Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution. J Chem Inf Model 2019; 59:2063-2078. [PMID: 30794388 DOI: 10.1021/acs.jcim.8b00940] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly widely utilized in studies of reactions in enzymes and other large systems. Here, we apply a range of QM/MM methods to investigate the Claisen rearrangement of chorismate to prephenate, in solution, and in the enzyme chorismate mutase. Using projector-based embedding in a QM/MM framework, we apply treatments up to the CCSD(T) level. We test a range of density functional QM/MM methods and QM region sizes. The results show that the calculated reaction energetics are significantly more sensitive to the choice of density functional than they are to the size of the QM region in these systems. Projector-based embedding of a wave function method in DFT reduced the 13 kcal/mol spread in barrier heights calculated at the DFT/MM level to a spread of just 0.3 kcal/mol, essentially eliminating dependence on the functional. Projector-based embedding of correlated ab initio methods provides a practical method for achieving high accuracy for energy profiles derived from DFT and DFT/MM calculations for reactions in condensed phases.
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Affiliation(s)
- Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Darya Shchepanovska
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Narin Lawan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Stephen J Macrae
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Jolanta Zurek
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
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41
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42
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Machado MR, Barrera EE, Klein F, Sóñora M, Silva S, Pantano S. The SIRAH 2.0 Force Field: Altius, Fortius, Citius. J Chem Theory Comput 2019; 15:2719-2733. [PMID: 30810317 DOI: 10.1021/acs.jctc.9b00006] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A new version of the coarse-grained (CG) SIRAH force field for proteins has been developed. Modifications to bonded and non-bonded interactions on the existing molecular topologies significantly ameliorate the structural description and flexibility of a non-redundant set of proteins. The SIRAH 2.0 force field has also been ported to the popular simulation package AMBER, which along with the former implementation in GROMACS expands significantly the potential range of users and performance of this CG force field on CPU/GPU codes. As a non-trivial example of its application, we undertook the structural and dynamical analysis of the most abundant and conserved calcium-binding protein, calmodulin (CaM). CaM is composed of two calcium-binding motifs called EF-hands, which in the presence of calcium specifically recognize a cognate peptide by embracing it. CG simulations of CaM bound to four calcium ions in the presence or absence of a binding peptide (holo and apo forms, respectively) resulted in good and stable ion coordination. The simulation of the holo form starting from an experimental structure sampled near-native conformations, retrieving quasi-atomistic precision. Removing the binding peptide enabled the EF-hands to perform large reciprocal movements, comparable to those observed in NMR structures. On the other hand, the isolated peptide starting from the helical conformation experienced spontaneous unfolding, in agreement with previous experimental data. However, repositioning the peptide in the neighborhood of one EF-hand not only prevented the peptide from unfolding but also drove CaM to a fully bound conformation, with both EF-hands embracing the cognate peptide, resembling the experimental holo structure. Therefore, SIRAH 2.0 shows the capacity to handle a number of structurally and dynamically challenging situations, including metal ion coordination, unbiased conformational sampling, and specific protein-peptide recognition.
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Affiliation(s)
- Matías R Machado
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Exequiel E Barrera
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Florencia Klein
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Martín Sóñora
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Steffano Silva
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
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43
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Bhowmik R, Sihn S, Varshney V, Roy AK, Vernon JP. Calculation of specific heat of polymers using molecular dynamics simulations. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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44
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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45
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Pedregal JR, Funes‐Ardoiz I, Sciortino G, Sánchez‐Aparicio J, Ujaque G, Lledós A, Maréchal J, Maseras F. GARLEEK: Adding an extra flavor to ONIOM. J Comput Chem 2018; 40:381-386. [DOI: 10.1002/jcc.25612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Jaime Rodríguez‐Guerra Pedregal
- Departament de QuímicaUniversitat Autònoma de Barcelona 08193 Bellaterra Catalonia Spain
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology Avgda. Països Catalans, 16, 43007, Tarragona Catalonia Spain
| | - Ignacio Funes‐Ardoiz
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology Avgda. Països Catalans, 16, 43007, Tarragona Catalonia Spain
| | - Giuseppe Sciortino
- Departament de QuímicaUniversitat Autònoma de Barcelona 08193 Bellaterra Catalonia Spain
| | | | - Gregori Ujaque
- Departament de QuímicaUniversitat Autònoma de Barcelona 08193 Bellaterra Catalonia Spain
| | - Agustí Lledós
- Departament de QuímicaUniversitat Autònoma de Barcelona 08193 Bellaterra Catalonia Spain
| | - Jean‐Didie Maréchal
- Departament de QuímicaUniversitat Autònoma de Barcelona 08193 Bellaterra Catalonia Spain
| | - Feliu Maseras
- Departament de QuímicaUniversitat Autònoma de Barcelona 08193 Bellaterra Catalonia Spain
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology Avgda. Països Catalans, 16, 43007, Tarragona Catalonia Spain
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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci 2018; 19:ijms19113496. [PMID: 30404229 PMCID: PMC6274762 DOI: 10.3390/ijms19113496] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
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47
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Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:20-37. [PMID: 30273615 DOI: 10.1016/j.pbiomolbio.2018.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023]
Abstract
While structural data on viruses are more and more common, information on their dynamics is much harder to obtain as those viruses form very large molecular complexes. In this paper, we propose a new method for computing the coarse-grained normal modes of such supra-molecules, NormalGo. A new formalism is developed to represent the Hessian of a quadratic potential using tensor products. This formalism is applied to the Tirion elastic potential, as well as to a Gō like potential. When combined with a fast method for computing a select set of eigenpairs of the Hessian, this new formalism enables the computation of thousands of normal modes of a full viral shell with more than one hundred thousand atoms in less than 2 h on a standard desktop computer. We then compare the two coarse-grained potentials. We show that, despite significant differences in their formulations, the Tirion and the Gō like potentials capture very similar dynamics characteristics of the molecule under study. However, we find that the Gō like potential should be preferred as it leads to less local deformations in the structure of the molecule during normal mode dynamics. Finally, we use NormalGo to characterize the structural transitions that occur when FAB fragments bind to the icosahedral outer shell of serotype 3 of the Dengue virus. We have identified residues at the surface of the outer shell that are important for the transition between the FAB-free and FAB-bound conformations, and therefore potentially useful for the design of antibodies to Dengue viruses.
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48
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Xu L, Xu Y, Cheung NH, Wong KY. Practical approach for beryllium atomic clusters: TD-DFT potential energy surfaces from equilibrium to dissociation for excited states of 2s → 2p. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2324-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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O’Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, Thomas LM, Glowacki BR, Sage R, Tew P, Wonnacott M, Bates P, Mulholland AJ, Glowacki DR. Sampling molecular conformations and dynamics in a multiuser virtual reality framework. SCIENCE ADVANCES 2018; 4:eaat2731. [PMID: 29963636 PMCID: PMC6025904 DOI: 10.1126/sciadv.aat2731] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/18/2018] [Indexed: 05/28/2023]
Abstract
We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures "on the fly" and to interact with other users in the same virtual environment. A series of controlled studies, in which participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. This framework should accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug development, synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where three-dimensional dynamics matter, spanning research and education.
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Affiliation(s)
- Michael O’Connor
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
| | - Helen M. Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Edward Dawn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Oussama Metatla
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Anne Roudaut
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Matthew Sutton
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Lisa May Thomas
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Department of Theatre, University of Bristol, Cantock’s Close, Bristol BS8 1UP, UK
| | - Becca Rose Glowacki
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- School of Art and Design, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Rebecca Sage
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Philip Tew
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Mark Wonnacott
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Phil Bates
- Oracle Cloud Development Centre, Tower Wharf, Cheese Lane, Bristol BS2 2JJ, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - David R. Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
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