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Conter G, Monti S, Barcaro G, Goddard WA, Fortunelli A. Functionalized Amorphous Carbon Materials via Reactive Molecular Dynamics Simulations. ACS APPLIED MATERIALS & INTERFACES 2024; 16:48043-48057. [PMID: 39205653 DOI: 10.1021/acsami.4c06527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
We derive a database of atomistic structural models of amorphous carbon materials endowed with exohedral functional groups. We start from phases previously derived using the DynReaxMas method for reactive molecular dynamics simulations, which exhibit atomistic and medium-length-scale features in excellent agreement with available experimental data. Given a generic input structure/phase, we develop postprocessing simulation algorithms mimicking experimental preparation protocols aimed at: (1) "curing" the phase to decrease the defect concentration; (2) automatically selecting the most reactive carbon atoms via interaction with a probe molecular species, and (3) stabilizing the phase by saturating the valence of carbon atoms with single-bond functional groups. Although we focus on oxygen-bearing functionalities, they can be replaced with other monovalent groups, such as -H, -COOH, -CHO, so that the protocol is quite general. We finally classify reactive sites in terms of their location within the structural framework and coordination environment (edges, tunnels, rings, aromatic carbons becoming aliphatic) and try to single out descriptors that correlate with tendency to functionalization.
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Affiliation(s)
- Giorgio Conter
- Consiglio Nazionale delle Ricerche, CNR-ICCOM, Pisa 56124, Italy
- Scuola Normale Superiore, Pisa 56126, Italy
| | - Susanna Monti
- Consiglio Nazionale delle Ricerche, CNR-ICCOM, Pisa 56124, Italy
| | | | - William A Goddard
- Materials and Process Simulation Center (MSC), California Institute of Technology, Pasadena, California 91125, United States
| | - Alessandro Fortunelli
- Consiglio Nazionale delle Ricerche, CNR-ICCOM, Pisa 56124, Italy
- Materials and Process Simulation Center (MSC), California Institute of Technology, Pasadena, California 91125, United States
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Shen H, Shen X, Wu Z. Simulating the isotropic Raman spectra of O-H stretching mode in liquid H 2O based on a machine learning potential: the influence of vibrational couplings. Phys Chem Chem Phys 2023; 25:28180-28188. [PMID: 37819214 DOI: 10.1039/d3cp03035k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
In this study, we trained a deep potential (DP) for H2O, an accurate machine learning (ML) potential. We performed molecular dynamics (MD) simulations of liquid water using the DP model (or DeePMD simulations). Our results showed that the DP model exhibits DFT-level accuracy, and the DeePMD simulation is a promising approach for modeling the structural properties of liquid water. Based on the DeePMD simulation trajectories, we calculated the isotropic Raman spectra of the O-H stretching mode using the surface-specific velocity-velocity correlation function (ssVVCF), showing that the DeePMD/ssVVCF approach can correctly capture the bimodal characteristics of the experimental Raman spectra, with one peak located near 3400 cm-1 and the other near 3250 cm-1. The success of the DeePMD/ssVVCF approach should be credited to (1) the DFT-level accuracy of the DP model for H2O, (2) the ssVVCF formulation considering the coupling between vibrational modes, and (3) non-Condon effects. Furthermore, the DeePMD simulations revealed that the anharmonic interactions between the coupled water molecules in the first and second hydration shells should play an essential role in the strong mixing of the H-O-H bending mode and the O-H stretching mode, leading to the delocalization of the O-H stretching band. In particular, increasing the strength of hydrogen bonds would enhance the bend-stretch coupling, leading to the red-shifting of the O-H vibrational spectra and the increase in the intensity of the shoulder around 3250 cm-1.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang 550018, China.
| | - Xu Shen
- National Center of Technology Innovation for Intelligent Design and Numerical Control, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhenhua Wu
- Department of Big Data and Artificial Intelligence, Guizhou Vocational Technology College of Electronics & Information, Kaili, 556000, China
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Karafiludis S, Scoppola E, Wolf SE, Kochovski Z, Matzdorff D, Van Driessche AES, Hövelmann J, Emmerling F, Stawski TM. Evidence for liquid-liquid phase separation during the early stages of Mg-struvite formation. J Chem Phys 2023; 159:134503. [PMID: 37787132 DOI: 10.1063/5.0166278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023] Open
Abstract
The precipitation of struvite, a magnesium ammonium phosphate hexahydrate (MgNH4PO4 · 6H2O) mineral, from wastewater is a promising method for recovering phosphorous. While this process is commonly used in engineered environments, our understanding of the underlying mechanisms responsible for the formation of struvite crystals remains limited. Specifically, indirect evidence suggests the involvement of an amorphous precursor and the occurrence of multi-step processes in struvite formation, which would indicate non-classical paths of nucleation and crystallization. In this study, we use synchrotron-based in situ x-ray scattering complemented by cryogenic transmission electron microscopy to obtain new insights from the earliest stages of struvite formation. The holistic scattering data captured the structure of an entire assembly in a time-resolved manner. The structural features comprise the aqueous medium, the growing struvite crystals, and any potential heterogeneities or complex entities. By analysing the scattering data, we found that the onset of crystallization causes a perturbation in the structure of the surrounding aqueous medium. This perturbation is characterized by the occurrence and evolution of Ornstein-Zernike fluctuations on a scale of about 1 nm, suggesting a non-classical nature of the system. We interpret this phenomenon as a liquid-liquid phase separation, which gives rise to the formation of the amorphous precursor phase preceding actual crystal growth of struvite. Our microscopy results confirm that the formation of Mg-struvite includes a short-lived amorphous phase, lasting >10 s.
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Affiliation(s)
- Stephanos Karafiludis
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstatter-Straße 11, 12489 Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Ernesto Scoppola
- Biomaterials, Hierarchical Structure of Biological and Bio-inspired Materials, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Stephan E Wolf
- Friedrich-Alexander University Erlangen-Nürnberg (FAU), Department of Materials Science and Engineering, Institute for Glass and Ceramics, Martensstr. 5, 91058 Erlangen, Germany
| | - Zdravko Kochovski
- Helmholtz-Zentrum Berlin for Materials and Energy, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - David Matzdorff
- Helmholtz-Zentrum Berlin for Materials and Energy, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Alexander E S Van Driessche
- Instituto Andaluz de Ciencias de la Tierra (IACT), CSIC - Universidad de Granada, Av. De las Palmeras 4, 18100 Armilla, Spain
| | - Jörn Hövelmann
- REMONDIS Production GmbH, Brunnenstraße 138, 44536 Lünen, Germany
| | - Franziska Emmerling
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstatter-Straße 11, 12489 Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Tomasz M Stawski
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstatter-Straße 11, 12489 Berlin, Germany
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Lanza G. Water model for hydrophobic cavities: structure and energy from quantum-chemical calculations. Phys Chem Chem Phys 2023; 25:6902-6913. [PMID: 36799662 DOI: 10.1039/d2cp05195h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This ab initio study aims to design a series of large water clusters having a hollow clathrate-like cage able to host hydrophobic solutes of various sizes. Starting from the (H2O)n (n = 18, 20, 24 and 28) hollow cages, water layers have been added in a stepwise manner in order to model the configuration of water molecules beyond the primary shell. The large (H2O)100, (H2O)120 and (H2O)140 clusters complete the hydrogen bonding network of the cage with optimal and regular tiling of the do-, tetra-decahedron and hexa-decahedron, respectively. This study is corroborated by an investigation of dense water clusters up to the (H2O)123 one, being highly consistent with experimental data on ice concerning the electronic and zero-point energies for aggregate formation at 0 K and enthalpy and entropy at 273 K. The cavity creation profoundly alters the orientation of water molecules compared with those found in dense clusters. Nevertheless, such a large reorganization is necessary to maximize the water-water attraction by making it similar to the one found in dense clusters. The cage formation is an endothermic process; however, the computed values are large compared with previous reports for hydrocarbon aqueous solutions. Larger clusters are required for a more fruitful comparison.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco e della Salute, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy.
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Masaya TW, Goulay F. A Molecular Dynamic Study of the Effects of Surface Partitioning on the OH Radical Interactions with Solutes in Multicomponent Aqueous Aerosols. J Phys Chem A 2023; 127:751-764. [PMID: 36639126 DOI: 10.1021/acs.jpca.2c07419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The surface-bulk partitioning of small saccharide and amide molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80 Å cubic water box containing a series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water bulk were examined at a molecular level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars and amides leads to the migration of the molecule toward the interface. Within the first 2 nm from the water surface, surface-active solutes lose their rotational freedom and adopt a preferred orientation with the alkyl group pointing toward the surface. The different packing within the interface leads to different solvation shell structures and enhanced interaction between the organic molecules and absorbed OH radicals. The simulations provide quantitative information about the dimension, composition, and organization of the air-water interface as well as about the nonreactive interaction of the OH radicals with the organic solutes. It suggests that increased concentrations, preferred orientations, and decreased solvation near the air-water surface may lead to differences in reactivities between surface-active and surface-inactive molecules. The results are important to explain how heterogeneous oxidation mechanisms and kinetics within interfaces may differ from those of the bulk.
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Affiliation(s)
- Tadini Wenyika Masaya
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26506, United States
| | - Fabien Goulay
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26506, United States
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Rouxel JR, Keefer D, Aleotti F, Nenov A, Garavelli M, Mukamel S. Coupled Electronic and Nuclear Motions during Azobenzene Photoisomerization Monitored by Ultrafast Electron Diffraction. J Chem Theory Comput 2022; 18:605-613. [DOI: 10.1021/acs.jctc.1c00792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jérémy R. Rouxel
- Department of Chemistry and Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
- Univ Lyon, UJM-Saint-Etienne, CNRS, Graduate School Optics Institute, Laboratoire Hubert Curien UMR 5516, Saint-Etienne, F-42023, France
| | - Daniel Keefer
- Department of Chemistry and Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale, Universitá degli Studi di Bologna, Viale del Risorgimento 4, Bologna, I-40136, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Universitá degli Studi di Bologna, Viale del Risorgimento 4, Bologna, I-40136, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Universitá degli Studi di Bologna, Viale del Risorgimento 4, Bologna, I-40136, Italy
| | - Shaul Mukamel
- Department of Chemistry and Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
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Fritsch B, Hutzler A, Wu M, Khadivianazar S, Vogl L, Jank MPM, März M, Spiecker E. Accessing local electron-beam induced temperature changes during in situ liquid-phase transmission electron microscopy. NANOSCALE ADVANCES 2021; 3:2466-2474. [PMID: 36134158 PMCID: PMC9419575 DOI: 10.1039/d0na01027h] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/18/2021] [Indexed: 05/26/2023]
Abstract
A significant electron-beam induced heating effect is demonstrated for liquid-phase transmission electron microscopy at low electron flux densities using Au nanoparticles as local nanothermometers. The obtained results are in agreement with theoretical considerations. Furthermore, the impact of beam-induced heating on radiolysis chemistry is estimated and the consequences of the effect are discussed.
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Affiliation(s)
- Birk Fritsch
- Electron Devices (LEB), Department of Electrical, Electronic and Communication Engineering, Friedrich-Alexander University Erlangen-Nürnberg (FAU) Cauerstraße 6 91058 Erlangen Germany
| | - Andreas Hutzler
- Electron Devices (LEB), Department of Electrical, Electronic and Communication Engineering, Friedrich-Alexander University Erlangen-Nürnberg (FAU) Cauerstraße 6 91058 Erlangen Germany
| | - Mingjian Wu
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Interdisciplinary Center for Nanostructured Films (IZNF), Department of Materials Science and Engineering, Friedrich-Alexander University Erlangen-Nürnberg (FAU) Cauerstraße 3 91058 Erlangen Germany
| | - Saba Khadivianazar
- Electron Devices (LEB), Department of Electrical, Electronic and Communication Engineering, Friedrich-Alexander University Erlangen-Nürnberg (FAU) Cauerstraße 6 91058 Erlangen Germany
| | - Lilian Vogl
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Interdisciplinary Center for Nanostructured Films (IZNF), Department of Materials Science and Engineering, Friedrich-Alexander University Erlangen-Nürnberg (FAU) Cauerstraße 3 91058 Erlangen Germany
| | - Michael P M Jank
- Fraunhofer Institute for Integrated Systems and Device Technology IISB Schottkystraße 10 91058 Erlangen Germany
| | - Martin März
- Electron Devices (LEB), Department of Electrical, Electronic and Communication Engineering, Friedrich-Alexander University Erlangen-Nürnberg (FAU) Cauerstraße 6 91058 Erlangen Germany
- Fraunhofer Institute for Integrated Systems and Device Technology IISB Schottkystraße 10 91058 Erlangen Germany
| | - Erdmann Spiecker
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Interdisciplinary Center for Nanostructured Films (IZNF), Department of Materials Science and Engineering, Friedrich-Alexander University Erlangen-Nürnberg (FAU) Cauerstraße 3 91058 Erlangen Germany
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