1
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Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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2
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Hadad RE, Roy A, Rabani E, Redmer R, Baer R. Stochastic density functional theory combined with Langevin dynamics for warm dense matter. Phys Rev E 2024; 109:065304. [PMID: 39020867 DOI: 10.1103/physreve.109.065304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/17/2024] [Indexed: 07/19/2024]
Abstract
This study overviews and extends a recently developed stochastic finite-temperature Kohn-Sham density functional theory to study warm dense matter using Langevin dynamics, specifically under periodic boundary conditions. The method's algorithmic complexity exhibits nearly linear scaling with system size and is inversely proportional to the temperature. Additionally, a linear-scaling stochastic approach is introduced to assess the Kubo-Greenwood conductivity, demonstrating exceptional stability for dc conductivity. Utilizing the developed tools, we investigate the equation of state, radial distribution, and electronic conductivity of hydrogen at a temperature of 30 000 K. As for the radial distribution functions, we reveal a transition of hydrogen from gaslike to liquidlike behavior as its density exceeds 4g/cm^{3}. As for the electronic conductivity as a function of the density, we identified a remarkable isosbestic point at frequencies around 7 eV, which may be an additional signature of a gas-liquid transition in hydrogen at 30 000 K.
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Affiliation(s)
| | | | - Eran Rabani
- Department of Chemistry, University of California, Berkeley, California 94720, USA; Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; and The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
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3
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Sidler D, Schnappinger T, Obzhirov A, Ruggenthaler M, Kowalewski M, Rubio A. Unraveling a Cavity-Induced Molecular Polarization Mechanism from Collective Vibrational Strong Coupling. J Phys Chem Lett 2024; 15:5208-5214. [PMID: 38717382 PMCID: PMC11103705 DOI: 10.1021/acs.jpclett.4c00913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024]
Abstract
We demonstrate that collective vibrational strong coupling of molecules in thermal equilibrium can give rise to significant local electronic polarizations in the thermodynamic limit. We do so by first showing that the full nonrelativistic Pauli-Fierz problem of an ensemble of strongly coupled molecules in the dilute-gas limit reduces in the cavity Born-Oppenheimer approximation to a cavity-Hartree equation for the electronic structure. Consequently, each individual molecule experiences a self-consistent coupling to the dipoles of all other molecules, which amount to non-negligible values in the thermodynamic limit (large ensembles). Thus, collective vibrational strong coupling can alter individual molecules strongly for localized "hotspots" within the ensemble. Moreover, the discovered cavity-induced polarization pattern possesses a zero net polarization, which resembles a continuous form of a spin glass (or better polarization glass). Our findings suggest that the thorough understanding of polaritonic chemistry, requires a self-consistent treatment of dressed electronic structure, which can give rise to numerous, so far overlooked, physical mechanisms.
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Affiliation(s)
- Dominik Sidler
- Laboratory
for Materials Simulations, Paul Scherrer
Institute, 5232 Villigen PSI, Switzerland
- Max
Planck Institute for the Structure and Dynamics of Matter and Center
for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- The
Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas Schnappinger
- Department
of Physics, Stockholm University, AlbaNova University Center, SE-106
91 Stockholm, Sweden
| | - Anatoly Obzhirov
- Max
Planck Institute for the Structure and Dynamics of Matter and Center
for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- The
Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Ruggenthaler
- Max
Planck Institute for the Structure and Dynamics of Matter and Center
for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- The
Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Markus Kowalewski
- Department
of Physics, Stockholm University, AlbaNova University Center, SE-106
91 Stockholm, Sweden
| | - Angel Rubio
- Max
Planck Institute for the Structure and Dynamics of Matter and Center
for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- The
Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center
for Computational Quantum Physics, Flatiron
Institute, 162 Fifth Avenue, New York, New York 10010, United States
- Nano-Bio
Spectroscopy Group, University of the Basque
Country (UPV/EHU), 20018 San Sebastián, Spain
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4
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de Lima Menezes G, Sales Bezerra K, Nobre Oliveira JI, Fontenele Araújo J, Soares Galvão D, Alves da Silva R, Vogel Saivish M, Laino Fulco U. Quantum mechanics insights into melatonin and analogs binding to melatonin MT 1 and MT 2 receptors. Sci Rep 2024; 14:10922. [PMID: 38740789 PMCID: PMC11091226 DOI: 10.1038/s41598-024-59786-x] [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: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Melatonin receptors MT1 and MT2 are G protein-coupled receptors that mediate the effects of melatonin, a hormone involved in circadian rhythms and other physiological functions. Understanding the molecular interactions between these receptors and their ligands is crucial for developing novel therapeutic agents. In this study, we used molecular docking, molecular dynamics simulations, and quantum mechanics calculation to investigate the binding modes and affinities of three ligands: melatonin (MLT), ramelteon (RMT), and 2-phenylmelatonin (2-PMT) with both receptors. Based on the results, we identified key amino acids that contributed to the receptor-ligand interactions, such as Gln181/194, Phe179/192, and Asn162/175, which are conserved in both receptors. Additionally, we described new meaningful interactions with Gly108/Gly121, Val111/Val124, and Val191/Val204. Our results provide insights into receptor-ligand recognition's structural and energetic determinants and suggest potential strategies for designing more optimized molecules. This study enhances our understanding of receptor-ligand interactions and offers implications for future drug development.
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Affiliation(s)
- Gabriela de Lima Menezes
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-400, Brazil
| | - Katyanna Sales Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
- Applied Physics Department, University of Campinas, Campinas, São Paulo, 13083-859, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
| | - John Fontenele Araújo
- Departamento de Fisiologia e Comportamento, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
| | - Douglas Soares Galvão
- Applied Physics Department, University of Campinas, Campinas, São Paulo, 13083-859, Brazil
| | - Roosevelt Alves da Silva
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí, GO, 75801-615, Brazil
| | - Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José Do Rio Preto, São José Do Rio, Preto, SP, 15090-000, Brazil
- Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Brazilian Biosciences National Laboratory, Campinas, SP, 13083-100, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil.
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-400, Brazil.
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5
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Peinado RDS, Saivish MV, Menezes GDL, Fulco UL, da Silva RA, Korostov K, Eberle RJ, Melo PA, Nogueira ML, Pacca CC, Arni RK, Coronado MA. The search for an antiviral lead molecule to combat the neglected emerging Oropouche virus. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100238. [PMID: 38745914 PMCID: PMC11090880 DOI: 10.1016/j.crmicr.2024.100238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Oropouche virus (OROV) is a member of the Peribunyaviridae family and the causative agent of a dengue-like febrile illness transmitted by mosquitoes. Although mild symptoms generally occur, complications such as encephalitis and meningitis may develop. A lack of proper diagnosis, makes it a potential candidate for new epidemics and outbreaks like other known arboviruses such as Dengue, Yellow Fever and Zika virus. The study of natural molecules as potential antiviral compounds is a promising alternative for antiviral therapies. Wedelolactone (WDL) has been demonstrated to inhibit some viral proteins and virus replication, making it useful to target a wide range of viruses. In this study, we report the in silico effects of WDL on the OROV N-terminal polymerase and its potential inhibitory effects on several steps of viral infection in mammalian cells in vitro, which revealed that WDL indeed acts as a potential inhibitor molecule against OROV infection.
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Affiliation(s)
- Rafaela dos Santos Peinado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP 15054-000, Brazil
| | - Marielena Vogel Saivish
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-100, Brazil
| | - Gabriela de Lima Menezes
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil
| | - Umberto Laino Fulco
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil
| | | | - Karolina Korostov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Raphael Josef Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf 40225, Germany
| | - Paulo A. Melo
- Departamento de Farmacologia Básica e Clínica - ICB, CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Maurício Lacerda Nogueira
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
- Sealy Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Carolina Colombelli Pacca
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
| | - Raghuvir Krishnaswamy Arni
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP 15054-000, Brazil
| | - Mônika Aparecida Coronado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP 15054-000, Brazil
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
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6
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Listyarini R, Kriesche BM, Hofer TS. Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H 2O. J Chem Theory Comput 2024; 20:3028-3045. [PMID: 38595064 PMCID: PMC11044269 DOI: 10.1021/acs.jctc.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute-solvent pair distribution function g(r) (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO2. When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.
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Affiliation(s)
- Risnita
Vicky Listyarini
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Bernhard M. Kriesche
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
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7
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Hicks CB, Martinez TJ. Massively scalable workflows for quantum chemistry: BigChem and ChemCloud. J Chem Phys 2024; 160:142501. [PMID: 38591672 DOI: 10.1063/5.0190834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Electronic structure theory, i.e., quantum chemistry, is the fundamental building block for many problems in computational chemistry. We present a new distributed computing framework (BigChem), which allows for an efficient solution of many quantum chemistry problems in parallel. BigChem is designed to be easily composable and leverages industry-standard middleware (e.g., Celery, RabbitMQ, and Redis) for distributed approaches to large scale problems. BigChem can harness any collection of worker nodes, including ones on cloud providers (such as AWS or Azure), local clusters, or supercomputer centers (and any mixture of these). BigChem builds upon MolSSI packages, such as QCEngine to standardize the operation of numerous computational chemistry programs, demonstrated here with Psi4, xtb, geomeTRIC, and TeraChem. BigChem delivers full utilization of compute resources at scale, offers a programable canvas for designing sophisticated quantum chemistry workflows, and is fault tolerant to node failures and network disruptions. We demonstrate linear scalability of BigChem running computational chemistry workloads on up to 125 GPUs. Finally, we present ChemCloud, a web API to BigChem and successor to TeraChem Cloud. ChemCloud delivers scalable and secure access to BigChem over the Internet.
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Affiliation(s)
- Colton B Hicks
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Todd J Martinez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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8
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Xu J, Carney TE, Zhou R, Shepard C, Kanai Y. Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics. J Am Chem Soc 2024; 146:5011-5029. [PMID: 38362887 DOI: 10.1021/jacs.3c08226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The explicit real-time propagation approach for time-dependent density functional theory (RT-TDDFT) has increasingly become a popular first-principles computational method for modeling various time-dependent electronic properties of complex chemical systems. In this Perspective, we provide a nontechnical discussion of how this first-principles simulation approach has been used to gain novel physical insights into nonequilibrium electron dynamics phenomena in recent years. Following a concise overview of the RT-TDDFT methodology from a practical standpoint, we discuss our recent studies on the electronic stopping of DNA in water and the Floquet topological phase as examples. Our discussion focuses on how RT-TDDFT simulations played a unique role in deriving new scientific understandings. We then discuss existing challenges and some new advances at the frontier of RT-TDDFT method development for studying increasingly complex dynamic phenomena and systems.
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Affiliation(s)
- Jianhang Xu
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas E Carney
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ruiyi Zhou
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Christopher Shepard
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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9
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Kedidi N, Ayadi T, Debbichi M. Bi-based bracelet-like monolayer with negative in-plane Poisson's ratio and enhanced photocatalytic performance: a first-principles study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:205503. [PMID: 38330467 DOI: 10.1088/1361-648x/ad2794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/08/2024] [Indexed: 02/10/2024]
Abstract
Auxetic materials are in high demand for advanced applications due to their relatively rare negative Poisson's ratio in two-dimensional materials. This study investigates the structural, mechanical, electronic, optical and photocatalytic properties of the AsBiTe3monolayer(ML) using first-principles calculations. Through analysis of phonon dispersion curves,ab-initiomolecular dynamics simulations, and Born conditions, we have confirmed the thermal, dynamic, and mechanical stability of the AsBiTe3monolayer. The study of the mechanical properties of this material revealed significant anisotropy and a bidirectional in-plane negative Poisson's ratio (NPR). In addition, electronic band structures calculated, with and without spin-orbit coupling (SOC) using the HSE functional, indicate that this monolayer exhibits the characteristics of an indirect-gap semiconductor around 1.17 and 1.32 eV, respectively. Notably, by assessing the optical properties of AsBiTe3monolayer, it has been found that this monolayer has a strong light-harvesting capability with an absorption coefficient higher than 105 cm-1in the visible region. Fascinatingly, under a biaxial 1%and 4%tensile and -2% compressive strain, the band edge of the AsBiTe3monolayer extends across the redox potential of water at pH = 0, 7 and 14, respectively. This suggests that this monolayer holds promise as a potential material for catalytic water splitting. These results should inspire further experimental and theoretical research, aimed at fully exploring the potential applications of this new class of 2D materials.
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Affiliation(s)
- N Kedidi
- Université de Monastir, Faculté des Sciences de Monastir, Laboratoire de la matière condensée et nanosciences LR11ES40, 5019 Monastir, Tunisia
| | - T Ayadi
- Université Paris-Saclay, CEA, Service de recherche en Corrosion et Comportement des Matériaux, SRMP, 91191 Gif-sur-Yvette, France
| | - M Debbichi
- Université de Monastir, Faculté des Sciences de Monastir, Laboratoire de la matière condensée et nanosciences LR11ES40, 5019 Monastir, Tunisia
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10
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Micoulaut M. Pockets, jumps and filaments: classifying ionic motion and determining the role of structure in electrochemical properties of 2Li 2S-GeS 2superionic glasses. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:195703. [PMID: 38316043 DOI: 10.1088/1361-648x/ad266d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
The structural properties of a typical solid electrolyte system (2Li2S-GeS2) is investigated from First principles molecular dynamics simulations. Results reveal that depolymerization of the base GeS2network by alkali additives takes place but appears reduced with respect to the corresponding sodium analog glass. Experimental structure functions are reproduced and reveal that the network is dominated by GeS4/2tetrahedra that are connected by edges (four-membered rings) and corners and disrupted by the addition of lithium, albeit a non-negligible fraction of connecting tetrahedra (Q2units) are still present in the glass structure. Dynamic and electric properties are also studied and emphasize that the size of the migrating cation (Li) is essential for ensuring a good level of ionic conductivity as it displays increased values with respect to the parent Na-bearing system. On the atomic (picosecond) timescale, different typical Li trajectories are identified and their distribution calculated: reduced cage-like motion in pockets constrained by the surrounding (Ge,S) network, back and forth jump motions with short transition states and long-range filamentary motion.
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Affiliation(s)
- Matthieu Micoulaut
- Sorbonne Université, Laboratoire de Physique Théorique de la Matiére Condensée, CNRS UMR 7600, 4 Place Jussieu, 75252 Paris Cedex 05, France
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11
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da Rocha JM, Campos DMDO, Esmaile SC, Menezes GDL, Bezerra KS, da Silva RA, Junior EDDS, Tayyeb JZ, Akash S, Fulco UL, Alqahtani T, Oliveira JIN. Quantum biochemical analysis of the binding interactions between a potential inhibitory drug and the Ebola viral glycoprotein. J Biomol Struct Dyn 2024:1-17. [PMID: 38258414 DOI: 10.1080/07391102.2024.2305314] [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: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
Ebola virus disease (EVD) causes outbreaks and epidemics in West Africa that persist until today. The envelope glycoprotein of Ebola virus (GP) consists of two subunits, GP1 and GP2, and plays a key role in anchoring or fusing the virus to the host cell in its active form on the virion surface. Toremifene (TOR) is a ligand that mainly acts as an estrogen receptor antagonist; however, a recent study showed a strong and efficient interaction with GP. In this context, we aimed to evaluate the energetic affinity features involved in the interaction between GP and toremifene by computer simulation techniques using the Molecular Fractionation Method with Conjugate Caps (MFCC) scheme and quantum-mechanical (QM) calculations, as well as missense mutations to assess protein stability. We identified ASP522, GLU100, TYR517, THR519, LEU186, LEU515 as the most attractive residues in the EBOV glycoprotein structure that form the binding pocket. We divided toremifene into three regions and evaluated that region i was more important than region iii and region ii for the formation of the TOR-GP1/GP2 complex, which might control the molecular remodeling process of TOR. The mutations that caused more destabilization were ARG134, LEU515, TYR517 and ARG559, while those that caused stabilization were GLU523 and ASP522. TYR517 is a critical residue for the binding of TOR, and is highly conserved among EBOV species. Our results may help to elucidate the mechanism of drug action on the GP protein of the Ebola virus and subsequently develop new pharmacological approaches against EVD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jaerdyson M da Rocha
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel M de O Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Stephany C Esmaile
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Gabriela de L Menezes
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Katyanna S Bezerra
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Roosevelt A da Silva
- Core Collaboratives of BioSistemas, Special Unit of Exact Sciences, Federal University of Jataí, Jataí, GO, Brazil
| | - Edilson D da S Junior
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Jehad Zuhair Tayyeb
- Department of Clinical Biochemistry, College of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, Bangladesh
| | - Umberto L Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Jonas I N Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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12
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Saivish MV, Menezes GDL, da Silva RA, de Assis LR, Teixeira IDS, Fulco UL, Avilla CMS, Eberle RJ, Santos IDA, Korostov K, Webber ML, da Silva GCD, Nogueira ML, Jardim ACG, Regasin LO, Coronado MA, Pacca CC. Acridones as promising drug candidates against Oropouche virus. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100217. [PMID: 38234431 PMCID: PMC10792649 DOI: 10.1016/j.crmicr.2023.100217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Abstract
Oropouche virus (OROV) is an emerging vector-borne arbovirus found in South America that causes Oropouche fever, a febrile infection similar to dengue fever. It has a high epidemic potential, causing illness in over 500,000 cases diagnosed since the virus was first discovered in 1955. Currently, the prevention of human viral infection depends on vaccination, but availability for many viruses is limited, and they are classified as neglected viruses. At present, there are no vaccines or antiviral treatments available. An alternative approach to limiting the spread of the virus is to selectively disrupt viral replication mechanisms. Here, we demonstrate the inhibitory effect of acridones, which efficiently inhibited viral replication by 99.9 % in vitro. To evaluate possible mechanisms of action, we conducted tests with dsRNA, an intermediate in virus replication, as well as MD simulations, docking, and binding free energy analysis. The results showed a strong interaction between FAC21 and the OROV endonuclease, which possibly limits the interaction of viral RNA with other proteins. Therefore, our results suggest a dual mechanism of antiviral action, possibly caused by ds-RNA intercalation. In summary, our findings demonstrate that a new generation of antiviral drugs could be developed based on the selective optimization of molecules.
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Affiliation(s)
- Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
| | - Gabriela de Lima Menezes
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí, GO 75801-615, Brazil
- Bioinformatics Multidisciplinary Environment, Programa de Pós-graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil
| | | | - Leticia Ribeiro de Assis
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
| | - Igor da Silva Teixeira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
| | - Umberto Laino Fulco
- Bioinformatics Multidisciplinary Environment, Programa de Pós-graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil
| | - Clarita Maria Secco Avilla
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
| | - Raphael Josef Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstraße, Düsseldorf 40225, Germany
| | - Igor de Andrade Santos
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia-MG 38405-302, Brazil
| | - Karolina Korostov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Mayara Lucia Webber
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
| | - Gislaine Celestino Dutra da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia-MG 38405-302, Brazil
| | - Luis Octavio Regasin
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
| | - Mônika Aparecida Coronado
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Carolina Colombelli Pacca
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
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13
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Mandova T, Saivish MV, Menezes GDL, Bezerra KS, Fulco UL, da Silva RA, Da Costa FB, Nogueira ML. Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus ( Peribunyaviridae). Pharmaceutics 2023; 15:2769. [PMID: 38140109 PMCID: PMC10747393 DOI: 10.3390/pharmaceutics15122769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The Oropouche virus (OROV) is a member of the family Peribunyaviridae (order Bunyavirales) and the cause of a dengue-like febrile illness transmitted mainly by biting midges and mosquitoes. In this study, we aimed to explore acylphloroglucinols and xanthohumol from hops (Humulus lupulus L.) as a promising alternative for antiviral therapies. The evaluation of the inhibitory potential of hops compounds on the viral cycle of OROV was performed through two complementary approaches. The first approach applies cell-based assay post-inoculation experiments to explore the inhibitory potential on the latest steps of the viral cycle, such as genome translation, replication, virion assembly, and virion release from the cells. The second part covers in silico methods evaluating the ability of those compounds to inhibit the activity of the endonuclease domain, which is essential for transcription, binding, and cleaving RNA. In conclusion, the beta acids showed strongest inhibitory potential in post-treatment assay (EC50 = 26.7 µg/mL). Xanthohumol had the highest affinity for OROV endonuclease followed by colupulone and cohumulone. This result contrasts with that observed for docking and MM/PBSA analysis, where cohumulone was found to have a higher affinity. Finally, among the three tested ligands, Lys92 and Arg33 exhibited the highest affinity with the protein.
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Affiliation(s)
- Tsvetelina Mandova
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
- Gilson Purification, 22 rue Bourseul, 56890 Saint Avé, France
| | - Marielena Vogel Saivish
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Gabriela de Lima Menezes
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Katyanna Sales Bezerra
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Umberto Laino Fulco
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | | | - Fernando Batista Da Costa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
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14
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Zahabi N, Baryshnikov G, Linares M, Zozoulenko I. Charge carrier dynamics in conducting polymer PEDOT using ab initio molecular dynamics simulations. J Chem Phys 2023; 159:154801. [PMID: 37843059 DOI: 10.1063/5.0169363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/01/2023] [Indexed: 10/17/2023] Open
Abstract
As conducting polymers become increasingly important in electronic devices, understanding their charge transport is essential for material and device development. Various semi-empirical approaches have been used to describe temporal charge carrier dynamics in these materials, but there have yet to be any theoretical approaches utilizing ab initio molecular dynamics. In this work, we develop a computational technique based on ab initio Car-Parrinello molecular dynamics to trace charge carrier temporal motion in archetypical conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT). Particularly, we analyze charge dynamics in a single PEDOT chain and in two coupled chains with different degrees of coupling and study the effect of temperature. In our model we first initiate a positively charged polaron (compensated by a negative counterion) at one end of the chain, and subsequently displace the counterion to the other end of the chain and trace polaron dynamics in the system by monitoring bond length alternation in the PEDOT backbone and charge density distribution. We find that at low temperature (T = 1 K) the polaron distortion gradually disappears from its initial location and reappears near the new position of the counterion. At the room temperature (T = 300 K), we find that the distortions induced by polaron, and atomic vibrations are of the same magnitude, which makes tracking the polaron distortion challenging because it is hidden behind the temperature-induced vibrations. The novel approach developed in this work can be used to study polaron mobility along and between the chains, investigate charge transport in highly doped polymers, and explore other flexible polymers, including n-doped ones.
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Affiliation(s)
- Najmeh Zahabi
- Laboratory of Organic Electronics (LOE), Department of Science and Technology (ITN), Campus Norrköping, Linköping University, SE-60174 Norrköping, Sweden
| | - Glib Baryshnikov
- Laboratory of Organic Electronics (LOE), Department of Science and Technology (ITN), Campus Norrköping, Linköping University, SE-60174 Norrköping, Sweden
| | - Mathieu Linares
- Group of Scientific Visualization, Department of Science and Technology (ITN), Campus Norrköping, Linköping University, SE-60174 Norrköping, Sweden
- Swedish e-Science Center (SeRC), Linköping University, SE-581 83 Linköping, Sweden
| | - Igor Zozoulenko
- Laboratory of Organic Electronics (LOE), Department of Science and Technology (ITN), Campus Norrköping, Linköping University, SE-60174 Norrköping, Sweden
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15
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Lourenço ACM, Santin LG, Fajemiroye JO, Oliveira SS, Napolitano HB. Studies on charge transfer of enalapril maleate: from solid-state to molecular dynamics. J Mol Model 2023; 29:197. [PMID: 37268806 DOI: 10.1007/s00894-023-05597-2] [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: 02/15/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023]
Abstract
INTRODUCTION Enalapril maleate is an antihypertensive ethyl ester pro-drug with two crystalline forms. A network of hydrogen bonds in both polymorphs plays an important role on solid-state stability, charge transfer process and degradation reactions (when exposed to high humidity, temperature and/or pH changes). COMPUTATIONAL PROCEDURES Supramolecular arrangement was proposed by Hirshfeld surface using the CrystalExplorer17 software and quantum theory of atoms in molecules. The electronic structure properties were calculated using the functional hybrid M06-2X with 6-311++G** base function employing diffuse and polarization functions to improve the description of hydrogen atoms on intermolecular interactions. Also, the H+ charge transfer between enalapril and maleate molecules was performed using Car-Parrinello molecular dynamics with the Verlet algorithm. In both simulations, the temperature of the ionic system was maintained around 300 K using the Nosé-Hoover thermostat and the electronic system evolved without the use of the thermostat. RESULTS This work evaluates the effect of maleate on the structural stability of enalapril maleate solid state. The electronic structural analysis points out a partially covalent character for N1-H∙∙∙O7 interaction; and the molecular dynamic showed a decentralized hydrogen on maleate driving a decomposition by charge transfer process while a centered hydrogen driving the stabilization. The charge transfer process and the mobility of the proton (H+) between enalapril and maleate molecules was demonstrated using supramolecular modeling analyses and molecular dynamics calculations.
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Affiliation(s)
- Ana Carolina M Lourenço
- Grupo de Química Teórica E Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Lauriane G Santin
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anápolis, GO, Brazil
| | - James O Fajemiroye
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anápolis, GO, Brazil
- Laboratório de Farmacologia de Produtos Naturais E Sintéticos, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Solemar S Oliveira
- Grupo de Química Teórica E Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Hamilton B Napolitano
- Grupo de Química Teórica E Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil.
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anápolis, GO, Brazil.
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16
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Niklasson AMN, Negre CFA. Shadow energy functionals and potentials in Born-Oppenheimer molecular dynamics. J Chem Phys 2023; 158:2882249. [PMID: 37093997 DOI: 10.1063/5.0146431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
In Born-Oppenheimer molecular dynamics (BOMD) simulations based on the density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which, in practice, never is fully converged. The calculated energies and forces are, therefore, only approximate, which may lead to an unphysical energy drift and instabilities. Here, we discuss an alternative shadow BOMD approach that is based on backward error analysis. Instead of calculating approximate solutions for an underlying exact regular Born-Oppenheimer potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow Born-Oppenheimer potential energy surface. In this way, the calculated forces are conservative with respect to the approximate shadow potential and generate accurate molecular trajectories with long-term energy stabilities. We show how such shadow Born-Oppenheimer potentials can be constructed at different levels of accuracy as a function of the integration time step, δt, from the constrained minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each energy functional, there is a corresponding ground state Born-Oppenheimer potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original "zeroth-level" shadow energy functionals and potentials used in extended Lagrangian BOMD [Niklasson, Eur. Phys. J. B 94, 164 (2021)]. The proposed shadow energy functionals and potentials are useful only within this extended dynamical framework, where also the electronic degrees of freedom are propagated as dynamical field variables together with the atomic positions and velocities. The theory is quite general and can be applied to MD simulations using approximate DFT, Hartree-Fock, or semi-empirical methods, as well as to coarse-grained flexible charge models.
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Affiliation(s)
- Anders M N Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Christian F A Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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17
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Saivish MV, Pacca CC, da Costa VG, de Lima Menezes G, da Silva RA, Nebo L, da Silva GCD, de Aguiar Milhim BHG, da Silva Teixeira I, Henrique T, Mistrão NFB, Hernandes VM, Zini N, de Carvalho AC, Fontoura MA, Rahal P, Sacchetto L, Marques RE, Nogueira ML. Caffeic Acid Has Antiviral Activity against Ilhéus Virus In Vitro. Viruses 2023; 15:494. [PMID: 36851709 PMCID: PMC9961518 DOI: 10.3390/v15020494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Ilhéus virus (ILHV) is a neglected mosquito-borne flavivirus. ILHV infection may lead to Ilhéus fever, an emerging febrile disease like dengue fever with the potential to evolve into a severe neurological disease characterized by meningoencephalitis; no specific treatments are available for this disease. This study assessed the antiviral properties of caffeic acid, an abundant component of plant-based food products that is also compatible with the socioeconomic limitations associated with this neglected infectious disease. The in vitro activity of caffeic acid on ILHV replication was investigated in Vero and A549 cell lines using plaque assays, quantitative RT-PCR, and immunofluorescence assays. We observed that 500 µM caffeic acid was virucidal against ILHV. Molecular docking indicated that caffeic acid might interact with an allosteric binding site on the envelope protein.
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Affiliation(s)
- Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Carolina Colombelli Pacca
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
- Faceres Medical School, São José do Rio Preto 15090-000, SP, Brazil
| | - Vivaldo Gomes da Costa
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
| | - Gabriela de Lima Menezes
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí 75801-615, GO, Brazil
| | | | - Liliane Nebo
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí 75801-615, GO, Brazil
| | - Gislaine Celestino Dutra da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Bruno Henrique Gonçalves de Aguiar Milhim
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Igor da Silva Teixeira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Tiago Henrique
- Laboratório de Marcadores Moleculares e Bioinformática, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Natalia Franco Bueno Mistrão
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Victor Miranda Hernandes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Nathalia Zini
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Ana Carolina de Carvalho
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Marina Alves Fontoura
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA
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18
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Structural Insights into Plasticity and Discovery of Flavonoid Allosteric Inhibitors of Flavivirus NS2B–NS3 Protease. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Flaviviruses are among the most critical pathogens in tropical regions; they cause various severe diseases in developing countries but are not restricted to these countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Ten proteins are encoded in the flavivirus RNA. The N2B–NS3pro protein complex plays a fundamental role in flavivirus replication and is a promising drug target; however, no flavivirus protease inhibitors have progressed to the preclinical stage. This study analyzed the structural models and plasticity of the NS2B–NS3pro protein complex of five medically important non-dengue flaviviruses (West Nile, Rocio, Ilhéus, yellow fever, and Saint Louis encephalitis). The flavonoids amentoflavone, tetrahydrorobustaflavone, and quercetin were selected for their exceptional binding energies as potential inhibitors of the NS2B–NS3pro protein complex. AutoDock Vina results ranged from −7.0 kcal/mol to −11.5 kcal/mol and the compounds preferentially acted non-competitively. Additionally, the first structural model for the NS2B–NS3pro protein complex was proposed for Ilhéus and Rocio viruses. The NS2B–NS3pro protease is an attractive molecular target for drug development. The three identified natural flavonoids showed great inhibitory potential against the viral species. Nevertheless, further in silico and in vitro studies are required to obtain more information regarding NS2B–NS3pro inhibition by these flavonoids and their therapeutic potential.
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19
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Cordier BA, Sawaya NPD, Guerreschi GG, McWeeney SK. Biology and medicine in the landscape of quantum advantages. J R Soc Interface 2022; 19:20220541. [PMID: 36448288 PMCID: PMC9709576 DOI: 10.1098/rsif.2022.0541] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
Quantum computing holds substantial potential for applications in biology and medicine, spanning from the simulation of biomolecules to machine learning methods for subtyping cancers on the basis of clinical features. This potential is encapsulated by the concept of a quantum advantage, which is contingent on a reduction in the consumption of a computational resource, such as time, space or data. Here, we distill the concept of a quantum advantage into a simple framework to aid researchers in biology and medicine pursuing the development of quantum applications. We then apply this framework to a wide variety of computational problems relevant to these domains in an effort to (i) assess the potential of practical advantages in specific application areas and (ii) identify gaps that may be addressed with novel quantum approaches. In doing so, we provide an extensive survey of the intersection of biology and medicine with the current landscape of quantum algorithms and their potential advantages. While we endeavour to identify specific computational problems that may admit practical advantages throughout this work, the rapid pace of change in the fields of quantum computing, classical algorithms and biological research implies that this intersection will remain highly dynamic for the foreseeable future.
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Affiliation(s)
- Benjamin A. Cordier
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97202, USA
| | | | | | - Shannon K. McWeeney
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97202, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97202, USA
- Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97202, USA
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20
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Yue L. Trajectory surface hopping molecular dynamics on Chemiluminescence of cyclic peroxides. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ling Yue
- Key Laboratory for Non‐Equilibrium Synthesis and Modulation of Condensed Matter, Ministry of Education, School of Chemistry Xi'an Jiaotong University Xi'an China
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21
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Mocci F, de Villiers Engelbrecht L, Olla C, Cappai A, Casula MF, Melis C, Stagi L, Laaksonen A, Carbonaro CM. Carbon Nanodots from an In Silico Perspective. Chem Rev 2022; 122:13709-13799. [PMID: 35948072 PMCID: PMC9413235 DOI: 10.1021/acs.chemrev.1c00864] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.
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Affiliation(s)
- Francesca Mocci
- Department
of Chemical and Geological Sciences, University
of Cagliari, I-09042 Monserrato, Italy,
| | | | - Chiara Olla
- Department
of Physics, University of Cagliari, I-09042 Monserrato, Italy
| | - Antonio Cappai
- Department
of Physics, University of Cagliari, I-09042 Monserrato, Italy
| | - Maria Francesca Casula
- Department
of Mechanical, Chemical and Materials Engineering, University of Cagliari, Via Marengo 2, IT 09123 Cagliari, Italy
| | - Claudio Melis
- Department
of Physics, University of Cagliari, I-09042 Monserrato, Italy
| | - Luigi Stagi
- Department
of Chemistry and Pharmacy, Laboratory of Materials Science and Nanotechnology, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Aatto Laaksonen
- Department
of Chemical and Geological Sciences, University
of Cagliari, I-09042 Monserrato, Italy,Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden,State Key
Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, P. R. China,Centre
of Advanced Research in Bionanoconjugates and Biopolymers, PetruPoni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda 41A, 700487 Iasi, Romania,Division
of Energy Science, Energy Engineering, Luleå
University of Technology, Luleå 97187, Sweden,
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22
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Saivish MV, Menezes GDL, da Costa VG, da Silva GCD, Marques RE, Nogueira ML, Silva RAD. Predicting Antigenic Peptides from Rocio Virus NS1 Protein for Immunodiagnostic Testing Using Immunoinformatics and Molecular Dynamics Simulation. Int J Mol Sci 2022; 23:7681. [PMID: 35887029 PMCID: PMC9322101 DOI: 10.3390/ijms23147681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022] Open
Abstract
The mosquito-borne disease caused by the Rocio virus is a neglected threat, and new immune inputs for serological testing are urgently required for diagnosis in low-resource settings and epidemiological surveillance. We used in silico approaches to identify a specific antigenic peptide (p_ROCV2) in the NS1 protein of the Rocio virus that was theoretically predicted to be stable and exposed on its surface, where it demonstrated key properties allowing it to interact with antibodies. These findings related to the molecular dynamics of this peptide provide important insights for advancing diagnostic platforms and investigating therapeutic alternatives.
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Affiliation(s)
- Marielena Vogel Saivish
- Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.); (G.C.D.d.S.)
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil;
| | - Gabriela de Lima Menezes
- Núcleo Colaborativo de Biosistemas, Universidade Federal de Jataí, Jataí 75801-615, GO, Brazil;
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil
| | - Vivaldo Gomes da Costa
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto 15054-000, SP, Brazil;
| | - Gislaine Celestino Dutra da Silva
- Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.); (G.C.D.d.S.)
| | - Rafael Elias Marques
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil;
| | - Maurício Lacerda Nogueira
- Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.); (G.C.D.d.S.)
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23
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Sidler D, Ruggenthaler M, Schäfer C, Ronca E, Rubio A. A perspective on ab initio modeling of polaritonic chemistry: The role of non-equilibrium effects and quantum collectivity. J Chem Phys 2022; 156:230901. [PMID: 35732522 DOI: 10.1063/5.0094956] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This Perspective provides a brief introduction into the theoretical complexity of polaritonic chemistry, which emerges from the hybrid nature of strongly coupled light-matter states. To tackle this complexity, the importance of ab initio methods is highlighted. Based on those, novel ideas and research avenues are developed with respect to quantum collectivity, as well as for resonance phenomena immanent in reaction rates under vibrational strong coupling. Indeed, fundamental theoretical questions arise about the mesoscopic scale of quantum-collectively coupled molecules when considering the depolarization shift in the interpretation of experimental data. Furthermore, to rationalize recent findings based on quantum electrodynamical density-functional theory (QEDFT), a simple, but computationally efficient, Langevin framework is proposed based on well-established methods from molecular dynamics. It suggests the emergence of cavity-induced non-equilibrium nuclear dynamics, where thermal (stochastic) resonance phenomena could emerge in the absence of external periodic driving. Overall, we believe that the latest ab initio results indeed suggest a paradigmatic shift for ground-state chemical reactions under vibrational strong coupling from the collective quantum interpretation toward a more local, (semi)-classically and non-equilibrium dominated perspective. Finally, various extensions toward a refined description of cavity-modified chemistry are introduced in the context of QEDFT, and future directions of the field are sketched.
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Affiliation(s)
- Dominik Sidler
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Ruggenthaler
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Schäfer
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Enrico Ronca
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), Via G. Moruzzi, 1, 56124 Pisa, Italy
| | - Angel Rubio
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
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24
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Simulation of Nuclear Quantum Effects in Condensed Matter Systems via Quantum Baths. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This paper reviews methods that aim at simulating nuclear quantum effects (NQEs) using generalized thermal baths. Generalized (or quantum) baths simulate statistical quantum features, and in particular zero-point energy effects, through non-Markovian stochastic dynamics. They make use of generalized Langevin Equations (GLEs), in which the quantum Bose–Einstein energy distribution is enforced by tuning the random and friction forces, while the system degrees of freedom remain classical. Although these baths have been formally justified only for harmonic oscillators, they perform well for several systems, while keeping the cost of the simulations comparable to the classical ones. We review the formal properties and main characteristics of classical and quantum GLEs, in relation with the fluctuation–dissipation theorems. Then, we describe the quantum thermostat and quantum thermal bath, the two generalized baths currently most used, providing several examples of applications for condensed matter systems, including the calculation of vibrational spectra. The most important drawback of these methods, zero-point energy leakage, is discussed in detail with the help of model systems, and a recently proposed scheme to monitor and mitigate or eliminate it—the adaptive quantum thermal bath—is summarised. This approach considerably extends the domain of application of generalized baths, leading, for instance, to the successful simulation of liquid water, where a subtle interplay of NQEs is at play. The paper concludes by overviewing further development opportunities and open challenges of generalized baths.
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25
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de Lima Menezes G, Vogel Saivish M, Lacerda Nogueira M, Alves da Silva R. Virtual screening of small natural compounds against NS1 protein of DENV, YFV and ZIKV. J Biomol Struct Dyn 2022; 41:2981-2991. [PMID: 35188085 DOI: 10.1080/07391102.2022.2042390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Diseases caused by viruses of the genus Flavivirus are among the main diseases that affect the world and they are a serious public health problem. Three of them stand out: Dengue, Yellow fever and Zika viruses. The non-structural protein 1 (NS1), encoded by this viral genus, in its dimeric form, plays important roles in the pathogenesis and RNA replication of these viruses. Therefore, the identification of chemicals with the potential to inhibit the formation of the NS1 protein dimer of DENV, YFV and ZIKV would enable them to act as a multi-target drug. For this, we selected conformations of the NS1 protein monomer with similar β-roll domain structure among the three virus species from conformations obtained from molecular dynamics simulations performed in GROMACS in 5 replicates of 150 ns for each species. After selecting the protein structures, a virtual screening of compounds from the natural products catalog of the ZINC database was performed using AutoDock Vina. The 100 best compounds were classified according efficiency criteria. Two compounds were observed in common to the species, with energy scores ranging from -9.2 kcal/mol to -10.1 kcal/mol. The results obtained here demonstrate the high similarity of NS1 proteins in the Flavivirus genus and high affinity for the same compounds; thus justifying the potential of these small molecules act in multitarget therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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26
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Macernis M, Streckaite S, Litvin R, Pascal AA, Llansola-Portoles MJ, Robert B, Valkunas L. Electronic and Vibrational Properties of Allene Carotenoids. J Phys Chem A 2022; 126:813-824. [PMID: 35114087 PMCID: PMC8859822 DOI: 10.1021/acs.jpca.1c09393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Carotenoids are conjugated
linear molecules built from the repetition
of terpene units, which display a large structural diversity in nature.
They may, in particular, contain several types of side or end groups,
which tune their functional properties, such as absorption position
and photochemistry. We report here a detailed experimental study of
the absorption and vibrational properties of allene-containing carotenoids,
together with an extensive modeling of these experimental data. Our
calculations can satisfactorily explain the electronic properties
of vaucheriaxanthin, where the allene group introduces the equivalent
of one C=C double bond into the conjugated C=C chain.
The position of the electronic absorption of fucoxanthin and butanoyloxyfucoxanthin
requires long-range corrections to be found correctly on the red side
of that of vaucheriaxanthin; however, these corrections tend to overestimate
the effect of the conjugated and nonconjugated C=O groups in
these molecules. We show that the resonance Raman spectra of these
carotenoids are largely perturbed by the presence of the allene group,
with the two major Raman contributions split into two components.
These perturbations are satisfactorily explained by modeling, through
a gain in the Raman intensity of the C=C antisymmetric stretching
mode, induced by the presence of the allene group in the carotenoid
C=C chain.
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Affiliation(s)
- Mindaugas Macernis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 3, LT-10222 Vilnius, Lithuania
| | - Simona Streckaite
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Radek Litvin
- Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Andrew A Pascal
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Manuel J Llansola-Portoles
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Bruno Robert
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 3, LT-10222 Vilnius, Lithuania.,Molecular Compounds Physics Department, Center for Physical Sciences and Technology, Sauletekio Avenue 3, LT-10257 Vilnius, Lithuania
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27
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:1077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
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28
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Penaloza-Amion M, C Rêgo CR, Wenzel W. Local Electronic Charge Transfer in the Helical Induction of Cis-Transoid Poly(4-carboxyphenyl)acetylene by Chiral Amines. J Chem Inf Model 2022; 62:544-552. [PMID: 35080886 DOI: 10.1021/acs.jcim.1c01347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Understanding the phenomena that lead to the formation of a specific helicity in helical polymers remains a challenge even today. Various polymers have been shown to assume different helical screw-senses depending on different stimuli. Acid-base chiral amines, for example, can induce helical conformations on cis-transoid poly(4-carboxyphenyl)acetylene yielding high-intensity circular dichroism signals. There have been many experimental attempts to elucidate the driving forces involved, but the induction process remains unclear. Here, we investigate the mechanism of helical polymer formation by both Molecular Dynamics (MD) and Density Functional Theory (DFT) approaches. We find that DFT calculations and the dissociation energies between 4 monomer polymers and amines show a clear trend in the affinity of R and S conformers with clockwise and counterclockwise polymer screw-senses, respectively. The charge analysis revealed that the local charge transfer effect plays a crucial role that leads to the helical polymer-amine induction.
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Affiliation(s)
- Montserrat Penaloza-Amion
- Institute of Nanotechnology Hermann-von-Helmholtz-Platz, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Celso R C Rêgo
- Institute of Nanotechnology Hermann-von-Helmholtz-Platz, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology Hermann-von-Helmholtz-Platz, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
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29
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Piccini G, Lee MS, Yuk SF, Zhang D, Collinge G, Kollias L, Nguyen MT, Glezakou VA, Rousseau R. Ab initio molecular dynamics with enhanced sampling in heterogeneous catalysis. Catal Sci Technol 2022. [DOI: 10.1039/d1cy01329g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enhanced sampling ab initio simulations enable to study chemical phenomena in catalytic systems including thermal effects & anharmonicity, & collective dynamics describing enthalpic & entropic contributions, which can significantly impact on reaction free energy landscapes.
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Affiliation(s)
- GiovanniMaria Piccini
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Istituto Eulero, Università della Svizzera italiana, Via Giuseppe Buffi 13, Lugano, Ticino, Switzerland
| | - Mal-Soon Lee
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Simuck F. Yuk
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Difan Zhang
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Greg Collinge
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Loukas Kollias
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Manh-Thuong Nguyen
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Vassiliki-Alexandra Glezakou
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Roger Rousseau
- Basic & Applied Molecular Foundations, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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30
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Abstract
The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this "on-the-fly" approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. This approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH2O → H2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.
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Affiliation(s)
- H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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31
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Finkelstein J, Smith JS, Mniszewski SM, Barros K, Negre CFA, Rubensson EH, Niklasson AMN. Quantum-Based Molecular Dynamics Simulations Using Tensor Cores. J Chem Theory Comput 2021; 17:6180-6192. [PMID: 34595916 DOI: 10.1021/acs.jctc.1c00726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary computational speed and energy efficiency but with the caveat that they were designed for tensor contractions (matrix-matrix multiplications) using only low-precision floating-point operations. Despite this perceived limitation, we demonstrate how tensor cores can be applied with high efficiency to the challenging and numerically sensitive problem of quantum-based Born-Oppenheimer molecular dynamics, which requires highly accurate electronic structure optimizations and conservative force evaluations. The interatomic forces are calculated on-the-fly from an electronic structure that is obtained from a generalized deep neural network, where the computational structure naturally takes advantage of the exceptional processing power of the tensor cores and allows for high performance in excess of 100 Tflops on a single Nvidia A100 GPU. Stable molecular dynamics trajectories are generated using the framework of extended Lagrangian Born-Oppenheimer molecular dynamics, which combines computational efficiency with long-term stability, even when using approximate charge relaxations and force evaluations that are limited in accuracy by the numerically noisy conditions caused by the low-precision tensor core floating-point operations. A canonical ensemble simulation scheme is also presented, where the additional numerical noise in the calculated forces is absorbed into a Langevin-like dynamics.
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Affiliation(s)
- Joshua Finkelstein
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States
| | - Justin S Smith
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States
| | - Susan M Mniszewski
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States
| | - Kipton Barros
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States
| | - Christian F A Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States
| | - Emanuel H Rubensson
- Division of Scientific Computing, Department of Information Technology, Uppsala University, Box 337, SE-751 05 Uppsala, Sweden
| | - Anders M N Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 New Mexico, United States
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32
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Abstract
Given the importance of catalysts in the chemical industry, they have been extensively investigated by experimental and numerical methods. With the development of computational algorithms and computer hardware, large-scale simulations have enabled influential studies with more atomic details reflecting microscopic mechanisms. This review provides a comprehensive summary of recent developments in molecular dynamics, including ab initio molecular dynamics and reaction force-field molecular dynamics. Recent research on both approaches to catalyst calculations is reviewed, including growth, dehydrogenation, hydrogenation, oxidation reactions, bias, and recombination of carbon materials that can guide catalyst calculations. Machine learning has attracted increasing interest in recent years, and its combination with the field of catalysts has inspired promising development approaches. Its applications in machine learning potential, catalyst design, performance prediction, structure optimization, and classification have been summarized in detail. This review hopes to shed light and perspective on ML approaches in catalysts.
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33
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Vieira SAPB, Dos Santos BM, Santos Júnior CD, de Paula VF, Gomes MSR, Ferreira GM, Gonçalves RL, Hirata MH, da Silva RA, Brandeburgo MIH, Mendes MM. Isohemigossypolone: Antiophidic properties of a naphthoquinone isolated from Pachira aquatica Aubl. Comp Biochem Physiol C Toxicol Pharmacol 2021; 245:109028. [PMID: 33676005 DOI: 10.1016/j.cbpc.2021.109028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 01/17/2023]
Abstract
We investigated the antiophidic properties of isohemigossypolone (ISO), a naphthoquinone isolated from the outer bark of the Pachira aquatic Aubl. The inhibition of phospholipase A2, coagulant, fibrinogenolytic, hemorrhagic and myotoxic activities induced by Bothrops pauloensis venom (Pb) was investigated. For this, we use samples resulting from the incubation of Pb with ISO in different concentrations (1:1, 1:5 and 1:10 w/w), we also evaluated the condition of treatment using ISO after 15 min of venom inoculation. The activities of phospholipase A2, coagulant, fibrinogenolytic, hemorrhagic and myotoxic induced by the B. pauloensis venom were significantly inhibited when the ISO was pre-incubated with the crude venom. For in vivo neutralization tests, the results were observed even when the ISO was applied after 15 min of inoculation of the venom or metalloprotease (BthMP). Also, to identify the inhibition mechanism, we performed in silico assays, across simulations of molecular coupling and molecular dynamics, it was possible to identify the modes of interaction between ISO and bothropic toxins BmooMPα-I, Jararacussin-I and BNSP-7. The present study shows that naphthoquinone isohemigossypolone isolated from the P. aquatica plant inhibited part of the local and systemic damage caused by venom proteins, demonstrating the pharmacological potential of this compound in neutralizing the harmful effects caused by snakebites.
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Affiliation(s)
| | - Benedito Matheus Dos Santos
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Célio Dias Santos Júnior
- Institute of Genetics and Biochemistry, Federal University of Uberlândia (UFU), Uberlândia, MG, Brazil
| | - Vanderlúcia Fonseca de Paula
- Laboratory of Natural Products, Department of Sciences and Technology, State University of Bahia Southwest (UESB), Jequié, BA, Brazil
| | - Mario Sergio Rocha Gomes
- Institute of Genetics and Biochemistry, Federal University of Uberlândia (UFU), Uberlândia, MG, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | | | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | | | | | - Mirian Machado Mendes
- Special Academic Unit of Biosciences, Federal University of Goiás (UFG), Jataí, GO, Brazil.
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34
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Zhang JH, Ricard TC, Haycraft C, Iyengar SS. Weighted-Graph-Theoretic Methods for Many-Body Corrections within ONIOM: Smooth AIMD and the Role of High-Order Many-Body Terms. J Chem Theory Comput 2021; 17:2672-2690. [PMID: 33891416 DOI: 10.1021/acs.jctc.0c01287] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a weighted-graph-theoretic approach to adaptively compute contributions from many-body approximations for smooth and accurate post-Hartree-Fock (pHF) ab initio molecular dynamics (AIMD) of highly fluxional chemical systems. This approach is ONIOM-like, where the full system is treated at a computationally feasible quality of treatment (density functional theory (DFT) for the size of systems considered in this publication), which is then improved through a perturbative correction that captures local many-body interactions up to a certain order within a higher level of theory (post-Hartree-Fock in this publication) described through graph-theoretic techniques. Due to the fluxional and dynamical nature of the systems studied here, these graphical representations evolve during dynamics. As a result, energetic "hops" appear as the graphical representation deforms with the evolution of the chemical and physical properties of the system. In this paper, we introduce dynamically weighted, linear combinations of graphs, where the transition between graphical representations is smoothly achieved by considering a range of neighboring graphical representations at a given instant during dynamics. We compare these trajectories with those obtained from a set of trajectories where the range of local many-body interactions considered is increased, sometimes to the maximum available limit, which yields conservative trajectories as the order of interactions is increased. The weighted-graph approach presents improved dynamics trajectories while only using lower-order many-body interaction terms. The methods are compared by computing dynamical properties through time-correlation functions and structural distribution functions. In all cases, the weighted-graph approach provides accurate results at a lower cost.
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Affiliation(s)
- Juncheng Harry Zhang
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Timothy C Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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35
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Quantum Chemical Microsolvation by Automated Water Placement. Molecules 2021; 26:molecules26061793. [PMID: 33806731 PMCID: PMC8005176 DOI: 10.3390/molecules26061793] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
We developed a quantitative approach to quantum chemical microsolvation. Key in our methodology is the automatic placement of individual solvent molecules based on the free energy solvation thermodynamics derived from molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). This protocol enabled us to rigorously define the number, position, and orientation of individual solvent molecules and to determine their interaction with the solute based on physical quantities. The generated solute-solvent clusters served as an input for subsequent quantum chemical investigations. We showcased the applicability, scope, and limitations of this computational approach for a number of small molecules, including urea, 2-aminobenzothiazole, (+)-syn-benzotriborneol, benzoic acid, and helicene. Our results show excellent agreement with the available ab initio molecular dynamics data and experimental results.
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36
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Niklasson AMN. Extended Lagrangian Born-Oppenheimer molecular dynamics for orbital-free density-functional theory and polarizable charge equilibration models. J Chem Phys 2021; 154:054101. [PMID: 33557538 DOI: 10.1063/5.0038190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for orbital-free Hohenberg-Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born-Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD.
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Affiliation(s)
- Anders M N Niklasson
- Theoretical Division T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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37
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Planas-Iglesias J, Marques SM, Pinto GP, Musil M, Stourac J, Damborsky J, Bednar D. Computational design of enzymes for biotechnological applications. Biotechnol Adv 2021; 47:107696. [PMID: 33513434 DOI: 10.1016/j.biotechadv.2021.107696] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their natural effectiveness has been fine-tuned as a result of millions of years of natural evolution. Such catalytic effectiveness has prompted the use of biocatalysts from multiple sources on different applications, including the industrial production of goods (food and beverages, detergents, textile, and pharmaceutics), environmental protection, and biomedical applications. Natural enzymes often need to be improved by protein engineering to optimize their function in non-native environments. Recent technological advances have greatly facilitated this process by providing the experimental approaches of directed evolution or by enabling computer-assisted applications. Directed evolution mimics the natural selection process in a highly accelerated fashion at the expense of arduous laboratory work and economic resources. Theoretical methods provide predictions and represent an attractive complement to such experiments by waiving their inherent costs. Computational techniques can be used to engineer enzymatic reactivity, substrate specificity and ligand binding, access pathways and ligand transport, and global properties like protein stability, solubility, and flexibility. Theoretical approaches can also identify hotspots on the protein sequence for mutagenesis and predict suitable alternatives for selected positions with expected outcomes. This review covers the latest advances in computational methods for enzyme engineering and presents many successful case studies.
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Affiliation(s)
- Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic; IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
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38
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Sahharova LT, Gordeev EG, Eremin DB, Ananikov VP. Pd-Catalyzed Synthesis of Densely Functionalized Cyclopropyl Vinyl Sulfides Reveals the Origin of High Selectivity in a Fundamental Alkyne Insertion Step. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Liliya T. Sahharova
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
| | - Evgeniy G. Gordeev
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
| | - Dmitry B. Eremin
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
- The Bridge@USC, University of Southern California, 1002 Childs Way, Los Angeles, California 90089-3502, United States
| | - Valentine P. Ananikov
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
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39
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de Lima Menezes G, da Silva RA. Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1). J Biomol Struct Dyn 2020; 39:5657-5667. [PMID: 32657643 PMCID: PMC7443570 DOI: 10.1080/07391102.2020.1792992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Non-structural protein 1 (nsp1) is found in all Betacoronavirus genus, an important viral group that causes severe respiratory
human diseases. This protein has significant role in pathogenesis and it is considered a
probably major virulence factor. As it is absent in humans, it becomes an interesting
target of study, especially when it comes to the rational search for drugs, since it
increases the specificity of the target and reduces possible adverse effects that may be
caused to the patient. Using approaches in silico we seek to
study the behavior of nsp1 in solution to obtain its most stable conformation and find
possible drugs with affinity to all of them. For this purpose, complete model of nsp1 of
SARS-CoV-2 were predicted and its stability analyzed by molecular dynamics simulations in
five different replicas. After main pocket validation using two control drugs and the main
conformations of nsp1, molecular docking based on virtual screening were performed to
identify novel potential inhibitors from DrugBank database. It has been found 16 molecules
in common to all five nsp1 replica conformations. Three of them was ranked as the best
compounds among them and showed better energy score than control molecules that have
in vitro activity against nsp1 from SARS-CoV-2. The
results pointed out here suggest new potential drugs for therapy to aid the rational drug
search against COVID-19. Communicated by Ramaswamy H. Sarma
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40
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Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, Laino T, Khaliullin RZ, Schütt O, Schiffmann F, Golze D, Wilhelm J, Chulkov S, Bani-Hashemian MH, Weber V, Borštnik U, Taillefumier M, Jakobovits AS, Lazzaro A, Pabst H, Müller T, Schade R, Guidon M, Andermatt S, Holmberg N, Schenter GK, Hehn A, Bussy A, Belleflamme F, Tabacchi G, Glöß A, Lass M, Bethune I, Mundy CJ, Plessl C, Watkins M, VandeVondele J, Krack M, Hutter J. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. J Chem Phys 2020; 152:194103. [PMID: 33687235 DOI: 10.1063/5.0007045] [Citation(s) in RCA: 924] [Impact Index Per Article: 231.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.
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Affiliation(s)
- Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mauro Del Ben
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Seewald
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Teodoro Laino
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, CH-801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Ole Schütt
- Department of Materials, ETH Zürich, CH-8092 Zürich, Switzerland
| | | | - Dorothea Golze
- Department of Applied Physics, Aalto University, Otakaari 1, FI-02150 Espoo, Finland
| | - Jan Wilhelm
- Institute of Theoretical Physics, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sergey Chulkov
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | | | - Valéry Weber
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | | | | | | | | | - Hans Pabst
- Intel Extreme Computing, Software and Systems, Zürich, Switzerland
| | - Tiziano Müller
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Robert Schade
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Manuel Guidon
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Samuel Andermatt
- Integrated Systems Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Nico Holmberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Gregory K Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Anna Hehn
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Augustin Bussy
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Belleflamme
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100 Como, Italy
| | - Andreas Glöß
- BASF SE, Carl-Bosch-Straße 38, D-67056 Ludwigshafen am Rhein, Germany
| | - Michael Lass
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Iain Bethune
- Hartree Centre, Science and Technology Facilities Council, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Christian Plessl
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Matt Watkins
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Joost VandeVondele
- Swiss National Supercomputing Centre (CSCS), ETH Zürich, Zürich, Switzerland
| | - Matthias Krack
- Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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41
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Niklasson AMN. Density-Matrix Based Extended Lagrangian Born–Oppenheimer Molecular Dynamics. J Chem Theory Comput 2020; 16:3628-3640. [DOI: 10.1021/acs.jctc.0c00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Anders M. N. Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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42
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Streckaite S, Macernis M, Li F, Kuthanová Trsková E, Litvin R, Yang C, Pascal AA, Valkunas L, Robert B, Llansola-Portoles MJ. Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution. J Phys Chem A 2020; 124:2792-2801. [PMID: 32163283 PMCID: PMC7313542 DOI: 10.1021/acs.jpca.9b11536] [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: 12/25/2022]
Abstract
![]()
Calculating
the spectroscopic properties of complex conjugated
organic molecules in their relaxed state is far from simple. An additional complexity arises for
flexible molecules in solution, where the rotational energy barriers
are low enough so that nonminimum conformations may become dynamically
populated. These metastable conformations quickly relax during the
minimization procedures preliminary to density functional theory calculations,
and so accounting for their contribution to the experimentally observed
properties is problematic. We describe a strategy for stabilizing
these nonminimum conformations in silico, allowing
their properties to be calculated. Diadinoxanthin and alloxanthin
present atypical vibrational properties in solution, indicating the
presence of several conformations. Performing energy calculations in vacuo and polarizable continuum model calculations in
different solvents, we found three different conformations with values
for the δ dihedral angle of the end ring ca. 0, 180, and 90°
with respect to the plane of the conjugated chain. The latter conformation,
a nonglobal minimum, is not stable during the minimization necessary
for modeling its spectroscopic properties. To circumvent this classical
problem, we used a Car–Parinello MD supermolecular approach,
in which diadinoxanthin was solvated by water molecules so that metastable
conformations were stabilized by hydrogen-bonding interactions. We
progressively removed the number of solvating waters to find the minimum
required for this stabilization. This strategy represents the first
modeling of a carotenoid in a distorted conformation and provides
an accurate interpretation of the experimental data.
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Affiliation(s)
- Simona Streckaite
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mindaugas Macernis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Ave. 3, LT-10222 Vilnius, Lithuania
| | - Fei Li
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.,Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, People's Republic of China
| | - Eliška Kuthanová Trsková
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.,Institute of Microbiology, Academy of Sciences of the Czech Republic, 379 81 Třeboň, Czech Republic
| | - Radek Litvin
- Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Chunhong Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, People's Republic of China
| | - Andrew A Pascal
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Ave. 3, LT-10222 Vilnius, Lithuania.,Molecular Compounds Physics Department, Center for Physical Sciences and Technology, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Manuel J Llansola-Portoles
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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43
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Niklasson AMN. Extended Lagrangian Born–Oppenheimer molecular dynamics using a Krylov subspace approximation. J Chem Phys 2020; 152:104103. [DOI: 10.1063/1.5143270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anders M. N. Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA and Division of Scientific Computing, Department of Information Technology, Uppsala University, Box 337, SE-751 05 Uppsala, Sweden
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44
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45
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e Silva KSF, Lima RM, Baeza LC, Lima PDS, Cordeiro TDM, Charneau S, da Silva RA, Soares CMDA, Pereira M. Interactome of Glyceraldehyde-3-Phosphate Dehydrogenase Points to the Existence of Metabolons in Paracoccidioides lutzii. Front Microbiol 2019; 10:1537. [PMID: 31338083 PMCID: PMC6629890 DOI: 10.3389/fmicb.2019.01537] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Paracoccidioides is a dimorphic fungus, the causative agent of paracoccidioidomycosis. The disease is endemic within Latin America and prevalent in Brazil. The treatment is based on azoles, sulfonamides and amphotericin B. The seeking for new treatment approaches is a real necessity for neglected infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential glycolytic enzyme, well known for its multitude of functions within cells, therefore categorized as a moonlight protein. To our knowledge, this is the first approach performed on the Paracoccidioides genus regarding the description of PPIs having GAPDH as a target. Here, we show an overview of experimental GAPDH interactome in different phases of Paracoccidioides lutzii and an in silico analysis of 18 proteins partners. GAPDH interacted with 207 proteins in P. lutzii. Several proteins bound to GAPDH in mycelium, transition and yeast phases are common to important pathways such as glycolysis and TCA. We performed a co-immunoprecipitation assay to validate the complex formed by GAPDH with triose phosphate isomerase, enolase, isocitrate lyase and 2-methylcitrate synthase. We found GAPDH participating in complexes with proteins of specific pathways, indicating the existence of a glycolytic and a TCA metabolon in P. lutzii. GAPDH interacted with several proteins that undergoes regulation by nitrosylation. In addition, we modeled the GAPDH 3-D structure, performed molecular dynamics and molecular docking in order to identify the interacting interface between GAPDH and the interacting proteins. Despite the large number of interacting proteins, GAPDH has only four main regions of contact with interacting proteins, reflecting its ancestrality and conservation over evolution.
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Affiliation(s)
| | - Raisa Melo Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lilian Cristiane Baeza
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Patrícia de Sousa Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Thuany de Moura Cordeiro
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Sébastien Charneau
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Roosevelt Alves da Silva
- Núcleo Colaborativo de Biossistemas, Instituto de Ciências Exatas, Universidade Federal de Jataí, Goiás, Brazil
| | | | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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46
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Martínez E, Perriot R, Kober EM, Bowlan P, Powell M, McGrane S, Cawkwell MJ. Parallel replica dynamics simulations of reactions in shock compressed liquid benzene. J Chem Phys 2019; 150:244108. [PMID: 31255087 DOI: 10.1063/1.5092209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The study of the long-term evolution of slow chemical reactions is challenging because quantum-based reactive molecular dynamics simulation times are typically limited to hundreds of picoseconds. Here, the extended Lagrangian Born-Oppenheimer molecular dynamics formalism is used in conjunction with parallel replica dynamics to obtain an accurate tool to describe the long-term chemical dynamics of shock-compressed benzene. Langevin dynamics has been employed at different temperatures to calculate the first reaction times in liquid benzene at pressures and temperatures consistent with its unreacted Hugoniot. Our coupled engine runs for times on the order of nanoseconds (one to two orders of magnitude longer than traditional techniques) and is capable of detecting reactions that are characterized by rates significantly slower than we could study before. At lower pressures and temperatures, we mainly observe Diels-Alder metastable reactions, whereas at higher pressures and temperatures we observe stable polymerization reactions.
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Affiliation(s)
- E Martínez
- Theoretical Division, T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R Perriot
- Theoretical Division, T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - E M Kober
- Theoretical Division, T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - P Bowlan
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M Powell
- Shock and Detonation Physics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S McGrane
- Shock and Detonation Physics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M J Cawkwell
- Theoretical Division, T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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47
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Bouchafra Y, Shee A, Réal F, Vallet V, Severo Pereira Gomes A. Predictive Simulations of Ionization Energies of Solvated Halide Ions with Relativistic Embedded Equation of Motion Coupled Cluster Theory. PHYSICAL REVIEW LETTERS 2018; 121:266001. [PMID: 30636145 DOI: 10.1103/physrevlett.121.266001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 06/09/2023]
Abstract
A subsystem approach for obtaining electron binding energies in the valence region is presented and applied to the case of halide ions (X^{-},X=F-At) in water. This approach is based on electronic structure calculations combining the relativistic equation-of-motion coupled cluster method for electron detachment and density functional theory via the frozen density embedding approach, using structures from classical molecular dynamics with polarizable force fields for discrete systems (in our study, droplets containing the anion and 50 water molecules). Our results indicate that one can accurately capture both the large solvent effect observed for the halides and the splitting of their ionization signals due to the increasingly large spin-orbit coupling of the p_{3/2}-p_{1/2} manifold across the series, at an affordable computational cost. Furthermore, owing to the quantum mechanical treatment of both solute and solvent electron binding energies of semiquantitative quality are also obtained for (bulk) water as by-products of the calculations for the halogens (in droplets).
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Affiliation(s)
- Yassine Bouchafra
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Avijit Shee
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Florent Réal
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Valérie Vallet
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - André Severo Pereira Gomes
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
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48
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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49
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Ricard TC, Iyengar SS. Efficiently Capturing Weak Interactions in ab Initio Molecular Dynamics with on-the-Fly Basis Set Extrapolation. J Chem Theory Comput 2018; 14:5535-5552. [DOI: 10.1021/acs.jctc.8b00803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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50
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Richters D, Kühne TD. Linear-scaling self-consistent field theory based molecular dynamics: application to C60buckyballs colliding with graphite. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1511899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Dorothee Richters
- Institute of Physical Chemistry and Center of Computational Sciences, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
- Paderborn Center for Parallel Computing and Institute for Lightweight Design with Hybrid Systems, Paderborn, Germany
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