1
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Wang Y, Sheng L, Xu B, Shi J, Chen Z. Study on Thermophysical Properties and Phase Change Regulation Mechanism of Optically-Controlled Phase Change Materials: Synthesis, Crystal Structure and Molecular Dynamics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404184. [PMID: 39128134 DOI: 10.1002/smll.202404184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/11/2024] [Indexed: 08/13/2024]
Abstract
Optically-controlled phase change materials, which are prepared by introducing molecular photoswitches into traditional phase change materials (PCMs), can convert and store solar energy into photochemical enthalpy and phase change enthalpy. However, the thermophysical properties of optically controlled PCMs, which are crucial in the practical, are rarely paid attention to. 4-(phenyldiazenyl)phenyl decanoate (Azo-A-10) is experimentally prepared as an optically-controlled PCMs, whose energy storage density is 210.0 kJ·kg-1, and the trans single crystal structure is obtained. The density, phase transition temperature, thermal conductivity, and other parameters in trans state are measured experimentally. Furthermore, a microscopic model of Azo-A-10 is established, and the thermophysical properties are analyzed based on molecular dynamics. The results show that the microstructure parameter (order parameters) and thermophysical properties (density, radial distribution function, self-diffusion coefficient, phase change temperature, and thermal conductivity) of partially or completely isomerized Azo-A-10, which are challenging to observe in experiments, can be predicted by molecular dynamics simulation. The optically-controlled phase change mechanism can be clarified according to the differences in microstructure. The optically-controlled switchability of thermophysical properties of an optically-controlled PCM is analyzed. This study provides ideas for the improvement, development, and application of optically-controlled PCMs in the future.
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Affiliation(s)
- Yi Wang
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Lisha Sheng
- College of Energy and Electrical Engineering, Hohai University, Nanjing, 210098, P. R. China
| | - Bo Xu
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Juan Shi
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Zhenqian Chen
- School of Energy and Environment, Southeast University, Nanjing, Jiangsu, 210096, China
- Jiangsu Province Key Laboratory of Solar Energy Science and Technology, Nanjing, Jiangsu, 210096, China
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2
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Huang Z, Gu C, Li J, Xiang P, Liao Y, Jiang BP, Ji S, Shen XC. Surface-Initiated Polymerization with an Initiator Gradient: A Monte Carlo Simulation. Polymers (Basel) 2024; 16:1203. [PMID: 38732672 PMCID: PMC11085584 DOI: 10.3390/polym16091203] [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: 03/21/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Due to the difficulty of accurately characterizing properties such as the molecular weight (Mn) and grafting density (σ) of gradient brushes (GBs), these properties are traditionally assumed to be uniform in space to simplify analysis. Applying a stochastic reaction model (SRM) developed for heterogeneous polymerizations, we explored surface-initiated polymerizations (SIPs) with initiator gradients in lattice Monte Carlo simulations to examine this assumption. An initial exploration of SIPs with 'homogeneously' distributed initiators revealed that increasing σ slows down the polymerization process, resulting in polymers with lower molecular weight and larger dispersity (Đ) for a given reaction time. In SIPs with an initiator gradient, we observed that the properties of the polymers are position-dependent, with lower Mn and larger Đ in regions of higher σ, indicating the non-uniform properties of polymers in GBs. The results reveal a significant deviation in the scaling behavior of brush height with σ compared to experimental data and theoretical predictions, and this deviation is attributed to the non-uniform Mn and Đ.
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Affiliation(s)
- Zhining Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China; (Z.H.); (B.-P.J.)
| | - Caixia Gu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China; (Z.H.); (B.-P.J.)
| | - Jiahao Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China; (Z.H.); (B.-P.J.)
| | - Peng Xiang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China; (Z.H.); (B.-P.J.)
| | - Yanda Liao
- School of Computer Science and Engineering & School of Software, Guangxi Normal University, Guilin 541004, China;
| | - Bang-Ping Jiang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China; (Z.H.); (B.-P.J.)
| | - Shichen Ji
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China; (Z.H.); (B.-P.J.)
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Xing-Can Shen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China; (Z.H.); (B.-P.J.)
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3
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Gődény M, Joerg F, Kovar MPP, Schröder C. Updates to Protex for Simulating Proton Transfers in an Ionic Liquid. J Phys Chem B 2024; 128:3416-3426. [PMID: 38557106 PMCID: PMC11017242 DOI: 10.1021/acs.jpcb.3c07356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The Python-based program Protex was initially developed for simulating proton transfers in a pure protic ionic liquid via polarizable molecular dynamics simulations. This method employs a single topology approach wherein deprotonated species retain a dummy atom, which is transformed into a real hydrogen atom during the protonation process. In this work, we extended Protex to include more intricate systems and to facilitate the simulation of the Grotthuss mechanism to enhance alignment with the empirical findings. The handling of proton transfer events within Protex was further refined for increased flexibility. In the original model, each deprotonated molecule contained a single dummy atom connected to the hydrogen acceptor atom. This model posed limitations for molecules with multiple atoms that could undergo protonation. To mitigate this issue, Protex was extended to execute a proton transfer when one of these potential atoms was within a suitable proximity for the transfer event. For the purpose of maintaining simplicity, Protex continues to utilize only a single dummy atom per deprotonated molecule. Another new feature pertains to the determination of the eligibility for a proton transfer event. A range of acceptable distances can now be defined within which the transfer probability is gradually turned off. These modifications allow for a more nuanced approach to simulating proton transfer events, offering greater accuracy and control of the modeling process.
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Affiliation(s)
- Márta Gődény
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- University
of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Straße 42, Vienna 1090, Austria
| | - Florian Joerg
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- University
of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Straße 42, Vienna 1090, Austria
| | - Maximilian P.-P. Kovar
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Christian Schröder
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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4
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Matamoros-Recio A, Alonso-Rueda E, Borrego E, Caballero A, Pérez PJ, Martín-Santamaría S. Molecular Dynamic Simulations of Aqueous Micellar Organometallic Catalysis: Methane Functionalization as a Case Study. Angew Chem Int Ed Engl 2024; 63:e202314773. [PMID: 38055325 DOI: 10.1002/anie.202314773] [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: 10/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/07/2023]
Abstract
Molecular Dynamics (MD) simulations constitute a powerful tool that provides a 3D perspective of the dynamical behavior of chemical systems. Herein the first MD study of the dynamics of a catalytic organometallic system, in micellar media, is presented. The challenging methane catalytic functionalization into ethyl propionate through a silver-catalyzed process has been targeted as the case study. The intimate nature of the micelles formed with the surfactants sodium dodecylsulfate (SDS) and potassium perfluorooctane sulfonate (PFOS) has been ascertained, as well as the relative distribution of the main actors in this transformation, namely methane, the diazo reagent and the silver catalyst, the latter in two different forms: the initial compound and a silver-carbene intermediate. Catalyst deactivation occurs with halide containing surfactants dodecyltrimethylammonium chloride (DTAC) and Triton X-100. Computed simulations allow explaining the experimental results, indicating that micelles behave differently regarding the degree of accumulation and the local distribution of the reactants and their effect in the molecular collisions leading to net reaction.
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Affiliation(s)
- Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Elia Alonso-Rueda
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Elena Borrego
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, 21007, Huelva, Spain
| | - Ana Caballero
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, 21007, Huelva, Spain
| | - Pedro J Pérez
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, 21007, Huelva, Spain
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
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5
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Ribeiro Junior LA, Pereira Junior ML, Fonseca AF. Elastocaloric Effect in Graphene Kirigami. NANO LETTERS 2023; 23:8801-8807. [PMID: 37477260 DOI: 10.1021/acs.nanolett.3c02260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Kirigami, a traditional Japanese art of paper cutting, has recently been explored for its elastocaloric effect (ECE) in kirigami-based materials (KMs), where an applied strain induces temperature changes. Importantly, the feasibility of a nanoscale graphene kirigami monolayer was experimentally demonstrated. Here, we investigate the ECE in GK representing the thinnest possible KM to better understand this phenomenon. Through molecular dynamics simulations, we analyze the temperature change and coefficient of performance (COP) of GK. Our findings reveal that while GKs lack the intricate temperature changes observed in macroscopic KMs, they exhibit a substantial temperature change of approximately 9.32 K (23 times higher than that of macroscopic KMs, which is about 0.4 K) for heating and -3.50 K for cooling. Furthermore, they demonstrate reasonable COP values of approximately 1.57 and 0.62, respectively. It is noteworthy that the one-atom-thick graphene configuration prevents the occurrence of the complex temperature distribution observed in macroscopic KMs.
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Affiliation(s)
- Luiz A Ribeiro Junior
- Institute of Physics, University of Brasília, 70910-900 Brasília, Brazil
- Computational Materials Laboratory, LCCMat, Institute of Physics, University of Brasília, 70910-900 Brasília, Brazil
| | - Marcelo L Pereira Junior
- Department of Electrical Engineering, Faculty of Technology, University of Brasília, 70910-900 Brasília, Brazil
| | - Alexandre F Fonseca
- Applied Physics Department, Gleb Wataghin Institute of Physics, University of Campinas, 13083-859 Campinas, São Paulo, Brazil
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6
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Li W. Molecular Dynamics Simulations of Ideal Living Polymerization: Terminal Model and Kinetic Aspects. J Phys Chem B 2023; 127:7624-7635. [PMID: 37642203 DOI: 10.1021/acs.jpcb.3c03126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Living polymerization is an important synthetic approach to achieving precise control of synthesized polymers, which is crucial for their applications. The molecular weight distribution (MWD) prescribes the macroscopic properties of polymers and hence is a key feature to characterize polymerization. In this work, we present a systematic molecular dynamics simulation study of ideal living polymerization in bulk and surface-initiated systems based on a terminal stochastic reaction model. The evolution of polymer dispersity and MWD along with the polymerization process is examined. We demonstrate that MWD is generally well captured by the Schulz-Zimm distribution for bulk and surface-initiated systems with low grafting densities. However, as the grafting density in the surface-initiated case increases, heterogeneity in chain growth emerges due to the kinetic trapping of reactive sites, which causes the starving of short chains and the thriving of minority long chains such that a shoulder region shows up in MWD. This effect can be enhanced by kinetic compressing induced by polymerization. In addition, the interplay of bonding reaction kinetics and other kinetic properties (e.g., mass transfer and polymer relaxation) is further explored, alongside the influences of bonding probability and reactant concentration. We expect that this investigation will aid in our understanding of typical kinetic aspects of living polymerization.
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Affiliation(s)
- Wei Li
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
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7
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Wang J, Xu X, Zheng L, Guo Q, Nie G. A signal "on-off-on"-type electrochemiluminescence aptamer sensor for detection of sulfadimethoxine based on Ru@Zn-oxalate MOF composites. Mikrochim Acta 2023; 190:131. [PMID: 36912979 DOI: 10.1007/s00604-023-05701-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023]
Abstract
An "on-off-on"-type electrochemiluminescence (ECL) aptamer sensor based on Ru@Zn-oxalate metal-organic framework (MOF) composites is constructed for sensitive detection of sulfadimethoxine (SDM). The prepared Ru@Zn-oxalate MOF composites with the three-dimensional structure provide good ECL performance for the "signal-on." The MOF structure with a large surface area enables the material to fix more Ru(bpy)32+. Moreover, the Zn-oxalate MOF with three-dimensional chromophore connectivity provides a medium which can accelerate excited-state energy transfer migration among Ru(bpy)32+ units, and greatly reduces the influence of solvent on chromophore, achieving a high-energy Ru emission efficiency. The aptamer chain modified with ferrocene at the end can hybridize with the capture chain DNA1 fixed on the surface of the modified electrode through base complementary pairing, which can significantly quench the ECL signal of Ru@Zn-oxalate MOF. SDM specifically binds to its aptamer to separate ferrocene from the electrode surface, resulting in a "signal-on" ECL signal. The use of the aptamer chain further improves the selectivity of the sensor. Thus, high-sensitivity detection of SDM specificity is realized through the specific affinity between SDM and its aptamer. This proposed ECL aptamer sensor has good analytical performance for SDM with low detection limit (27.3 fM) and wide detection range (100 fM-500 nM). The sensor also shows excellent stability, selectivity, and reproducibility, which proved its analytical performance. The relative standard deviation (RSD) of SDM detected by the sensor is between 2.39 and 5.32%, and the recovery is in the range 97.23 to 107.5%. The sensor shows satisfactory results in the analysis of actual seawater samples, which is expected to play a role in the exploration of marine environmental pollution.
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Affiliation(s)
- Jingjing Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Xuejiao Xu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Lu Zheng
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Qingfu Guo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Guangming Nie
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China.
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8
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Nishimura Y, Nakai H. Species-selective nanoreactor molecular dynamics simulations based on linear-scaling tight-binding quantum chemical calculations. J Chem Phys 2023; 158:054106. [PMID: 36754823 DOI: 10.1063/5.0132573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Here, extensions to quantum chemical nanoreactor molecular dynamics simulations for discovering complex reactive events are presented. The species-selective algorithm, where the nanoreactor effectively works for the selected desired reactants, was introduced to the original scheme. Moreover, for efficient simulations of large model systems with the modified approach, the divide-and-conquer linear-scaling density functional tight-binding method was exploited. Two illustrative applications of the polymerization of propylene and cyclopropane mixtures and the aggregation of sodium chloride from aqueous solutions indicate that species-selective quantum chemical nanoreactor molecular dynamics is a promising method to accelerate the sampling of multicomponent chemical processes proceeding under relatively mild conditions.
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Affiliation(s)
- Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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9
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Zhang Y, Lin Q, Jiang B. Atomistic neural network representations for chemical dynamics simulations of molecular, condensed phase, and interfacial systems: Efficiency, representability, and generalization. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yaolong Zhang
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
| | - Qidong Lin
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
| | - Bin Jiang
- Department of Chemical Physics, School of Chemistry and Materials Science, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes University of Science and Technology of China Hefei Anhui China
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10
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Sultana A, Kathuria A, Gaikwad KK. Metal-organic frameworks for active food packaging. A review. ENVIRONMENTAL CHEMISTRY LETTERS 2022; 20:1479-1495. [PMID: 35035339 PMCID: PMC8748186 DOI: 10.1007/s10311-022-01387-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 01/02/2022] [Indexed: 05/07/2023]
Abstract
Food wastage is a major concern for sustainable health and agriculture. To reduce food waste, classical preservation techniques such as drying, pasteurization, freeze-drying, fermentation, and microwave are available. Nonetheless, these techniques display shortcomings such as alteration of food and taste. Such shortcomings may be solved by active food packaging, which involves the incorporation of active agents into the packaging material. Recently, metal-organic frameworks, a class of porous hybrid supramolecular materials, have been developed as an active agent to extend food shelf life and maintain safety. Here, we review metal-organic frameworks in active packaging as oxygen scavengers, antimicrobials, moisture absorbers, and ethylene scavengers. We present methods of incorporation of metal-organic frameworks into packaging materials and their applications.
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Affiliation(s)
- Afreen Sultana
- Department of Paper Technology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 India
| | - Ajay Kathuria
- Industrial of Technology and Packaging, California Polytechnic State University, San Luis Obispo, CA 93407 USA
| | - Kirtiraj K. Gaikwad
- Department of Paper Technology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 India
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11
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Bley M, Baul U, Dzubiella J. Controlling solvent quality by time: Self-avoiding sprints in nonequilibrium polymerization. Phys Rev E 2021; 104:034501. [PMID: 34654077 DOI: 10.1103/physreve.104.034501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/22/2021] [Indexed: 12/20/2022]
Abstract
A fundamental paradigm in polymer physics is that macromolecular conformations in equilibrium can be described by universal scaling laws, being key for structure, dynamics, and function of soft (biological) matter and in the materials sciences. Here we reveal that during diffusion-influenced, nonequilibrium chain-growth polymerization, scaling laws change qualitatively, in particular, the growing polymers exhibit a surprising self-avoiding walk behavior in poor and θ solvents. Our analysis, based on monomer-resolved, off-lattice reaction-diffusion computer simulations, demonstrates that this phenomenon is a result of (i) nonequilibrium monomer density depletion correlations around the active polymerization site, leading to a locally directed and self-avoiding growth, in conjunction with (ii) chain (Rouse) relaxation times larger than the competing polymerization reaction time. These intrinsic nonequilibrium mechanisms are facilitated by fast and persistent reaction-driven diffusion ("sprints") of the active site, with analogies to pseudochemotactic active Brownian particles. Our findings have implications for time-controlled structure formation in polymer processing, as in, e.g., reactive self-assembly, photocrosslinking, and three-dimensional printing.
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Affiliation(s)
- Michael Bley
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany
| | - Upayan Baul
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany.,Cluster of Excellence livMats@FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, D-79110 Freiburg, Germany
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12
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Bachmann J, Doltsinis NL. Adaptive partitioning molecular dynamics using an extended Hamiltonian approach. J Chem Phys 2021; 155:144104. [PMID: 34654314 DOI: 10.1063/5.0059206] [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
A recently proposed extended Hamiltonian approach to switching interaction potentials is generalized to enable adaptive partitioning molecular dynamics simulations. Switching is performed along a fictitious classical degree of freedom whose value determines the mixing ratio of the two potentials on a time scale determined by its associated mass. We propose to choose this associated fictitious mass adaptively so as to ensure a constant time scale for all switching processes. For different model systems, including a harmonic oscillator and a Lennard-Jones fluid, we investigate the window of switching time scales that guarantees the conservation of the extended Hamiltonian for a large number of switching events. The methodology is first applied in the microcanonical ensemble and then generalized to the canonical ensemble using a Nosé-Hoover chain thermostat. It is shown that the method is stable for thousands of consecutive switching events during a single simulation, with constant temperature and a conserved extended Hamiltonian. A slight modification of the original Hamiltonian is introduced to avoid accumulation of small numerical errors incurred after each switching process.
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Affiliation(s)
- Jim Bachmann
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany
| | - Nikos L Doltsinis
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany
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13
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Torres-Knoop A, Kryven I. Learning heterogenous reaction rates from stochastic simulations. Phys Rev E 2021; 103:052402. [PMID: 34134324 DOI: 10.1103/physreve.103.052402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/10/2021] [Indexed: 11/07/2022]
Abstract
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by complex dynamical systems reproducing spatial movements of molecules and their collisions. Such molecular dynamics systems may implicitly capture intricate phenomena that affect reaction rates but are not accounted for in the macroscopic models. In this work we present a data assimilation procedure for learning nonhomogeneous kinetic parameters from molecular simulations with many simultaneously reacting species. The learned parameters can then be plugged into the deterministic reaction rate equations to predict long time evolution of the macroscopic system. In this way, our procedure discovers an effective differential equation for reaction kinetics. To demonstrate the procedure, we upscale the kinetics of a molecular system that forms a complex covalently bonded network severely interfering with the reaction rates. Incidentally, we report that the kinetic parameters of this system feature peculiar time and temperature dependences, whereas the probability of a network strand to close a cycle follows a universal distribution.
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Affiliation(s)
| | - Ivan Kryven
- Mathematical Institute, Utrecht University, Budapestlaan 6, 3508 TA Utrecht, Netherlands and Centre for Complex Systems Studies, 3584 CE Utrecht, Netherlands
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14
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Abstract
Machine learning (ML) techniques applied to chemical reactions have a long history. The present contribution discusses applications ranging from small molecule reaction dynamics to computational platforms for reaction planning. ML-based techniques can be particularly relevant for problems involving both computation and experiments. For one, Bayesian inference is a powerful approach to develop models consistent with knowledge from experiments. Second, ML-based methods can also be used to handle problems that are formally intractable using conventional approaches, such as exhaustive characterization of state-to-state information in reactive collisions. Finally, the explicit simulation of reactive networks as they occur in combustion has become possible using machine-learned neural network potentials. This review provides an overview of the questions that can and have been addressed using machine learning techniques, and an outlook discusses challenges in this diverse and stimulating field. It is concluded that ML applied to chemistry problems as practiced and conceived today has the potential to transform the way with which the field approaches problems involving chemical reactions, in both research and academic teaching.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland.,Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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15
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Biedermann M, Diddens D, Heuer A. Connecting the quantum and classical mechanics simulation world: Applications of reactive step molecular dynamics simulations. J Chem Phys 2021; 154:194105. [PMID: 34240915 DOI: 10.1063/5.0048618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This article presents the application of the reactive step molecular dynamics simulation method [M. Biedermann, D. Diddens, and A. Heuer, J. Chem. Theory Comput. 17, 1074 (2021)] toward two different atomistic, chemically reactive systems. During reactive steps, transitions from reactant to product molecules are modeled according to physically correct transition probabilities based on quantum chemical information about the reactions such as molecular reaction rates via instant exchange of the employed force field and a subsequent, short relaxation of the structure. In the first application, we study the follow-up reactions of singly reduced ethylene carbonate (EC) radicals in EC solution, first, via extensive ab initio molecular dynamics simulations and, second, with the reactive step algorithm. A direct comparison of both simulation methods shows excellent agreement. Then, we employ the reactive step algorithm to simulate the enolate formation of 2-methylcyclopropanone with the base lithium diisopropylamine. Thereby, we can demonstrate that the reactive step algorithm is also capable of capturing effects from kinetic vs thermodynamic control of chemical reactions during simulation.
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Affiliation(s)
- Myra Biedermann
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, GermanyHelmholtz-Institute Münster: Ionics in Energy Storage (IEK-12), Forschungszentrum Jülich GmbH, Corrensstrasse 46, 48149 Münster, Germany
| | - Diddo Diddens
- Helmholtz-Institute Münster: Ionics in Energy Storage (IEK-12), Forschungszentrum Jülich GmbH, Corrensstrasse 46, 48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, Germany
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16
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Biedermann M, Diddens D, Heuer A. rs@md: Introducing Reactive Steps at the Molecular Dynamics Simulation Level. J Chem Theory Comput 2021; 17:1074-1085. [DOI: 10.1021/acs.jctc.0c01189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myra Biedermann
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, Germany
| | - Diddo Diddens
- Helmholtz-Institute Münster Ionics in Energy Storage (IEK-12), Forschungszentrum Jülich GmbH, Corrensstrasse 46, 48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, Germany
- Helmholtz-Institute Münster Ionics in Energy Storage (IEK-12), Forschungszentrum Jülich GmbH, Corrensstrasse 46, 48149 Münster, Germany
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17
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Scivetti I, Sen K, Elena AM, Todorov I. Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble. J Phys Chem A 2020; 124:7585-7597. [PMID: 32820921 DOI: 10.1021/acs.jpca.0c05461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.
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Affiliation(s)
- Ivan Scivetti
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K.,Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - Kakali Sen
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
| | - Alin M Elena
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
| | - Ilian Todorov
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
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18
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Rice BM, Mattson WD, Larentzos JP, Byrd EFC. Heuristics for chemical species identification in dense systems. J Chem Phys 2020; 153:064102. [DOI: 10.1063/5.0015664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Betsy M. Rice
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
| | - William D. Mattson
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
| | - James P. Larentzos
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
| | - Edward F. C. Byrd
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
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19
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Käser S, Unke OT, Meuwly M. Isomerization and decomposition reactions of acetaldehyde relevant to atmospheric processes from dynamics simulations on neural network-based potential energy surfaces. J Chem Phys 2020; 152:214304. [DOI: 10.1063/5.0008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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20
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Abstract
The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.
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Affiliation(s)
- Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
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21
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Zhang Z, DuBay KH. Modeling the Influence of Emergent and Self-Limiting Phase Separations among Nascent Oligomers on Polymer Sequences Formed during Irreversible Step-Growth Copolymerizations. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhongmin Zhang
- Department of Chemistry, The University of Virginia, Charlottesville, Virginia, United States
| | - Kateri H. DuBay
- Department of Chemistry, The University of Virginia, Charlottesville, Virginia, United States
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22
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Reactive Molecular Dynamics Study of the Thermal Decomposition of Phenolic Resins. JOURNAL OF COMPOSITES SCIENCE 2019. [DOI: 10.3390/jcs3020032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The thermal decomposition of polyphenolic resins was studied by reactive molecular dynamics (RMD) simulation at elevated temperatures. Atomistic models of the polyphenolic resins to be used in the RMD were constructed using an automatic method which calls routines from the software package Materials Studio. In order to validate the models, simulated densities and heat capacities were compared with experimental values. The most suitable combination of force field and thermostat for this system was the Forcite force field with the Nosé–Hoover thermostat, which gave values of heat capacity closest to those of the experimental values. Simulated densities approached a final density of 1.05–1.08 g/cm3 which compared favorably with the experimental values of 1.16–1.21 g/cm3 for phenol-formaldehyde resins. The RMD calculations were run using LAMMPS software at temperatures of 1250 K and 3000 K using the ReaxFF force field and employing an in-house routine for removal of products of condensation. The species produced during RMD correlated with those found experimentally for polyphenolic systems and rearrangements to form cyclopropane moieties were observed. At the end of the RMD simulations a glassy carbon char resulted.
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23
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Roncero O, Zanchet A, Aguado A. Low temperature reaction dynamics for CH 3OH + OH collisions on a new full dimensional potential energy surface. Phys Chem Chem Phys 2018; 20:25951-25958. [PMID: 30294740 PMCID: PMC6290987 DOI: 10.1039/c8cp04970j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Is the rise of the rate constant measured in laval expansion experiments of OH with organic molecules at low temperatures due to the reaction between the reactants or due to the formation of complexes with the buffer gas? This question has importance for understanding the evolution of prebiotic molecules observed in different astrophysical objects. Among these molecules methanol is one of the most widely observed, and its reaction with OH has been studied by several groups showing a fast increase in the rate constant under 100 K. Transition state theory doesn't reproduce this behavior and here dynamical calculations are performed on a new full dimensional potential energy surface developed for this purpose. The calculated classical reactive cross sections show an increase at low collision energies due to a complex forming mechanism. However, the calculated rate constant at temperatures below 100 K remains lower than the observed one. Quantum effects are likely responsible for the measured behavior at low temperatures.
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Affiliation(s)
- Octavio Roncero
- Instituto de Física Fundamental (IFF-CSIC), C.S.I.C., Serrano 123, Madrid 28006, Spain.
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24
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Zhang Z, Krajniak J, Samaey G, Nies E. A Parallel Multiscale Simulation Framework for Complex Polymerization: AB
2
‐Type Monomer Hyperbranched Polymerization as an Example. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zidan Zhang
- Division of Polymer Chemistry and Materials, Department of ChemistryKatholieke Universiteit LeuvenCelestijnenlaan 200F B‐3001 Heverlee Belgium
| | - Jakub Krajniak
- Department of Computer ScienceKatholieke Universiteit LeuvenCelestijnenlaan 200A B‐3001 Heverlee Belgium
| | - Giovanni Samaey
- Department of Computer ScienceKatholieke Universiteit LeuvenCelestijnenlaan 200A B‐3001 Heverlee Belgium
| | - Erik Nies
- Division of Polymer Chemistry and Materials, Department of ChemistryKatholieke Universiteit LeuvenCelestijnenlaan 200F B‐3001 Heverlee Belgium
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25
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Sotriffer C. Docking of Covalent Ligands: Challenges and Approaches. Mol Inform 2018; 37:e1800062. [PMID: 29927068 DOI: 10.1002/minf.201800062] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Covalent ligands have recently regained considerable attention in drug discovery. The rational design of such ligands, however, is still faced with particular challenges, mostly related to the fact that covalent bond formation is a quantum mechanical phenomenon which cannot adequately be handled by the force fields or empirical approaches typically used for noncovalent protein-ligand interactions. Although the necessity for quantum chemical approaches is clear, they cannot yet routinely be applied on large data sets of ligands or for a broader exploration of binding modes in docking calculations. On the other hand, technical solutions for performing docking calculations with covalent ligands are available, but their scope is normally quite limited. Scoring functions typically neglect the contribution from covalent bond formation completely. In this situation, the question arises how to approach covalent ligands and which methods to choose for their docking and design.
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Affiliation(s)
- Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, D-, 97074, Würzburg, Germany
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26
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Krajniak J, Zhang Z, Pandiyan S, Nies E, Samaey G. Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions. J Comput Chem 2018; 39:1764-1778. [DOI: 10.1002/jcc.25348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/07/2018] [Accepted: 04/12/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Jakub Krajniak
- KU Leuven Department of Computer Science; Celestijnenlaan 200A; Leuven 3001 Belgium
| | - Zidan Zhang
- KU Leuven Division of Polymer Chemistry and Materials, Department of Chemistry; Celestijnenlaan 200F; Leuven 3001 Belgium
| | - Sudharsan Pandiyan
- KU Leuven Division of Polymer Chemistry and Materials, Department of Chemistry; Celestijnenlaan 200F; Leuven 3001 Belgium
| | - Eric Nies
- KU Leuven Division of Polymer Chemistry and Materials, Department of Chemistry; Celestijnenlaan 200F; Leuven 3001 Belgium
| | - Giovanni Samaey
- KU Leuven Department of Computer Science; Celestijnenlaan 200A; Leuven 3001 Belgium
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27
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Mattox TI, Larentzos JP, Moore SG, Stone CP, Ibanez DA, Thompson AP, Lísal M, Brennan JK, Plimpton SJ. Highly scalable discrete-particle simulations with novel coarse-graining: accessing the microscale. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1471532] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Timothy I. Mattox
- Engility Corporation, DoD High Performance Computing Modernization Program (HPCMP) PETTT Group, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA
| | - James P. Larentzos
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA
| | - Stan G. Moore
- Multiscale Science Department, Sandia National Laboratories, Albuquerque, NM, USA
| | - Christopher P. Stone
- Computational Science and Engineering, LLC, DoD High Performance Computing Modernization Program (HPCMP) PETTT Group, U.S. Air Force Research Laboratory, Dayton, OH, USA
| | - Daniel A. Ibanez
- Computational Multiphysics Department, Sandia National Laboratories, Albuquerque, NM, USA
| | - Aidan P. Thompson
- Multiscale Science Department, Sandia National Laboratories, Albuquerque, NM, USA
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Prague, Czech Republic
- Department of Physics, Faculty of Science, J. E. Purkinje University, Ústí n. Lab., Czech Republic
| | - John K. Brennan
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA
| | - Steven J. Plimpton
- Multiscale Science Department, Sandia National Laboratories, Albuquerque, NM, USA
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28
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Torres-Knoop A, Kryven I, Schamboeck V, Iedema PD. Modeling the free-radical polymerization of hexanediol diacrylate (HDDA): a molecular dynamics and graph theory approach. SOFT MATTER 2018; 14:3404-3414. [PMID: 29667682 DOI: 10.1039/c8sm00451j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the printing, coating and ink industries, photocurable systems are becoming increasingly popular and multi-functional acrylates are one of the most commonly used monomers due to their high reactivity (fast curing). In this paper, we use molecular dynamics and graph theory tools to investigate the thermo-mechanical properties and topology of hexanediol diacrylate (HDDA) polymer networks. The gel point was determined as the point where a giant component was formed. For the conditions of our simulations, we found the gel point to be around 0.18 bond conversion. A detailed analysis of the network topology showed, unexpectedly, that the flexibility of the HDDA molecules plays an important role in increasing the conversion of double bonds, while delaying the gel point. This is due to a back-biting type of reaction mechanism that promotes the formation of small cycles. The glass transition temperature for several degrees of curing was obtained from the change in the thermal expansion coefficient. For a bond conversion close to experimental values we obtained a glass transition temperature around 400 K. For the same bond conversion we estimate a Young's modulus of 3 GPa. Both of these values are in good agreement with experiments.
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Affiliation(s)
- Ariana Torres-Knoop
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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29
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Zanchet A, Del Mazo P, Aguado A, Roncero O, Jiménez E, Canosa A, Agúndez M, Cernicharo J. Full dimensional potential energy surface and low temperature dynamics of the H 2CO + OH → HCO + H 2O reaction. Phys Chem Chem Phys 2018; 20:5415-5426. [PMID: 28959812 PMCID: PMC6031300 DOI: 10.1039/c7cp05307j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new method is proposed to analytically represent the potential energy surface of reactions involving polyatomic molecules capable of accurately describing long-range interactions and saddle points, needed to describe low-temperature collisions. It is based on two terms, a reactive force field term and a many-body term. The reactive force field term accurately describes the fragments, long-range interactions among them and the saddle points for reactions. The many-body term increases the desired accuracy everywhere else. This method has been applied to the OH + H2CO → H2O + HCO reaction, giving a barrier of 27.4 meV. The simulated classical rate constants with this potential are in good agreement with recent experimental results [Ocaña et al., Astrophys. J., 2017, submitted], showing an important increase at temperatures below 100 K. The reaction mechanism is analyzed in detail here, and explains the observed behavior at low energy by the formation of long-lived collision complexes, with roaming trajectories, with a capture observed for very long impact parameters, >100 a.u., determined by the long-range dipole-dipole interaction.
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Affiliation(s)
- Alexandre Zanchet
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, c/Serrano 123, 28006 Madrid, Spain.
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30
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Radue MS, Jensen BD, Gowtham S, Klimek-McDonald DR, King JA, Odegard GM. Comparing the Mechanical Response of Di-, Tri-, and Tetra-functional Resin Epoxies with Reactive Molecular Dynamics. ACTA ACUST UNITED AC 2018; 56:255-264. [PMID: 31806922 DOI: 10.1002/polb.24539] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The influence of monomer functionality on the mechanical properties of epoxies is studied using Molecular Dynamics (MD) with the Reax Force Field (ReaxFF). From deformation simulations, the Young's modulus, yield point, and Poisson's ratio are calculated and analyzed. The results demonstrate an increase in stiffness and yield strength with increasing resin functionality. Comparison between the network structures of distinct epoxies is further advanced by the Monomeric Degree Index (MDI). Experimental validation demonstrates the MD results correctly predict the relationship in Young's moduli. Therefore, ReaxFF is confirmed to be a useful tool for studying the mechanical behavior of epoxies.
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Affiliation(s)
- M S Radue
- Michigan Technological University, Houghton, MI 49931
| | - Benjamin D Jensen
- Michigan Technological University, Houghton, MI 49931.,NASA Langley Research Center, Hampton, VA 23666
| | - S Gowtham
- Michigan Technological University, Houghton, MI 49931
| | | | - J A King
- Michigan Technological University, Houghton, MI 49931
| | - G M Odegard
- Michigan Technological University, Houghton, MI 49931
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31
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Steffen J, Hartke B. Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields. J Chem Phys 2017; 147:161701. [DOI: 10.1063/1.4979712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Zheng S, Javidpour L, Shing KS, Sahimi M. Dynamics of proteins aggregation. I. Universal scaling in unbounded media. J Chem Phys 2017; 145:134306. [PMID: 27782447 DOI: 10.1063/1.4962837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
It is well understood that in some cases proteins do not fold correctly and, depending on their environment, even properly-folded proteins change their conformation spontaneously, taking on a misfolded state that leads to protein aggregation and formation of large aggregates. An important factor that contributes to the aggregation is the interactions between the misfolded proteins. Depending on the aggregation environment, the aggregates may take on various shapes forming larger structures, such as protein plaques that are often toxic. Their deposition in tissues is a major contributing factor to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and prion. This paper represents the first part in a series devoted to molecular simulation of protein aggregation. We use the PRIME, a meso-scale model of proteins, together with extensive discontinuous molecular dynamics simulation to study the aggregation process in an unbounded fluid system, as the first step toward MD simulation of the same phenomenon in crowded cellular environments. Various properties of the aggregates have been computed, including dynamic evolution of aggregate-size distribution, mean aggregate size, number of peptides that contribute to the formation of β sheets, number of various types of hydrogen bonds formed in the system, radius of gyration of the aggregates, and the aggregates' diffusivity. We show that many of such quantities follow dynamic scaling, similar to those for aggregation of colloidal clusters. In particular, at long times the mean aggregate size S(t) grows with time as, S(t) ∼ tz, where z is the dynamic exponent. To our knowledge, this is the first time that the qualitative similarity between aggregation of proteins and colloidal aggregates has been pointed out.
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Affiliation(s)
- Size Zheng
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Leili Javidpour
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
| | - Katherine S Shing
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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33
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Larentzos JP, Rice BM. Transferable Reactive Force Fields: Extensions of ReaxFF-lg to Nitromethane. J Phys Chem A 2017; 121:2001-2013. [DOI: 10.1021/acs.jpca.6b11761] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- James P. Larentzos
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Betsy M. Rice
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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34
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Liu H, Zhu YL, Lu ZY, Müller-Plathe F. A kinetic chain growth algorithm in coarse-grained simulations. J Comput Chem 2016; 37:2634-2646. [DOI: 10.1002/jcc.24495] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/04/2016] [Accepted: 09/07/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Hong Liu
- State Key Laboratory of Supramolecular Structure and Materials; Institute of Theoretical Chemistry, Jilin University; Changchun 130021 China
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität; Darmstadt 64287 Deutschland
| | - You-Liang Zhu
- State Key Laboratory of Polymer Physics and Chemistry; Changchun Institute of Applied Chemistry, Chinese Academy of Sciences; Changchun 130022 China
| | - Zhong-Yuan Lu
- State Key Laboratory of Supramolecular Structure and Materials; Institute of Theoretical Chemistry, Jilin University; Changchun 130021 China
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität; Darmstadt 64287 Deutschland
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35
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Voyiatzis E, Böhm MC. Atomic and global mechanical properties of systems described by the Stillinger-Weber potential. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:325201. [PMID: 27345739 DOI: 10.1088/0953-8984/28/32/325201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Analytical expressions for the stress and elasticity tensors of materials, in which the interactions are described by the Stillinger-Weber potential, are derived in the context of the stress fluctuation formalism. The derived formulas can be used both in Monte Carlo and molecular dynamics simulations. As an example of possible applications, they are employed to calculate the influence of the temperature and system size on the mechanical properties of crystalline cubic boron nitride. The system has been studied by molecular dynamics simulations. The computed mechanical properties are in good agreement with available experimental data and first principle calculations. In the studied crystalline cubic boron nitride system, the employed formalism is of higher accuracy than the 'small-strain' non-equilibrium method. The dominant contributions to the elastic constants stem from the Born and stress fluctuation terms. An increase in the system size reduces the statistical uncertainties in the computation of the mechanical properties. A rise of the temperature leads to a slight increase in the observed uncertainties. The derived expressions for the stress and elasticity tensors are further decomposed into sums of atomic level stress and atomic level elasticity tensors. The developed factorization enables us (i) to quantify the contribution of the various chemical groups, in the case under consideration of the different atoms, to the observed mechanical properties and (ii) to determine the elastic constants with reduced computational uncertainties. The reason is that the exact values of some terms of the proposed factorization can be determined theoretically beforehand. Thus, they can be substituted in the derived formulas leading to an enhanced convergence.
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Affiliation(s)
- Evangelos Voyiatzis
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
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36
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Fetisov E, Kuo IFW, Knight C, VandeVondele J, Van Voorhis T, Siepmann JI. First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors. ACS CENTRAL SCIENCE 2016; 2:409-15. [PMID: 27413785 PMCID: PMC4919768 DOI: 10.1021/acscentsci.6b00095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 05/13/2023]
Abstract
Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. The equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data.
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Affiliation(s)
- Evgenii
O. Fetisov
- Department
of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - I-Feng William Kuo
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Knight
- Leadership
Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Joost VandeVondele
- Department
of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, 8093 Zurich, Switzerland
| | - Troy Van Voorhis
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Building 6-229, Cambridge, Massachusetts 02139-4307, United States
| | - J. Ilja Siepmann
- Department
of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
- Department
of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455-0132, United States
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37
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Influence of density and environmental factors on decomposition kinetics of amorphous polylactide – Reactive molecular dynamics studies. J Mol Graph Model 2016; 67:54-61. [DOI: 10.1016/j.jmgm.2016.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/18/2016] [Accepted: 04/29/2016] [Indexed: 11/22/2022]
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Alaghemandi M, Green JR. Reactive symbol sequences for a model of hydrogen combustion. Phys Chem Chem Phys 2016; 18:2810-7. [PMID: 26729563 DOI: 10.1039/c5cp05125h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transient, macroscopic states of chemical disequilibrium are born out of the microscopic dynamics of molecules. As a reaction mixture evolves, the temporal patterns of chemical species encodes some of this dynamical information, while their statistics are a manifestation of the bulk kinetics. Here, we define a chemically-informed symbolic dynamics as a coarse-grained representation of classical molecular dynamics, and analyze the sequences of chemical species for a model of hydrogen combustion. We use reactive molecular dynamics simulations to generate the sequences and derive probability distributions for sequence observables: the reaction time scales and the chain length - the total number of reactions between initiation of a reactant and termination at products. The time scales and likelihood of the sequences depend strongly on the chain length, temperature, and density. Temperature suppresses the uncertainty in chain length for hydrogen sequences, but enhances the uncertainty in oxygen sequence chain lengths. This method of analyzing a surrogate chemical symbolic dynamics reduces the complexity of the chemistry from the atomistic to the molecular level and has the potential for extension to more complicated reaction systems.
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Affiliation(s)
- Mohammad Alaghemandi
- Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125, USA.
| | - Jason R Green
- Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125, USA. and Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
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39
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Langeloth M, Sugii T, Böhm MC, Müller-Plathe F. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution. J Chem Phys 2015; 143:243158. [DOI: 10.1063/1.4937627] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Michael Langeloth
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt, Germany
| | - Taisuke Sugii
- Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034, Japan
| | - Michael C. Böhm
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt, Germany
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40
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Ekesan S, Herzfeld J. Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties. Proc Math Phys Eng Sci 2015. [DOI: 10.1098/rspa.2015.0370] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The monotonic and non-monotonic variations of atomic properties within and between the rows of the periodic table underlie our understanding of chemistry and accounting for these variations has been a signature strength of quantum mechanics (QM). However, the computational burden of QM motivates the development of more efficient means of describing electrons and reactivity. The recently developed LEWIS
•
model incorporates lessons learnt from QM into a force field that includes electrons as explicit pseudo-classical particles. Here, we extend LEWIS
•
across the 2
p
and 3
p
elements, and show that it is capable of reproducing both monotonic and non-monotonic variations of chemically important atomic properties in a cost-effective manner. An indicator of the strength of the construct is the ability of pairwise potentials trained on ionization energies and the order of spin configurations to predict atomic polarizabilities. In this manner, some insights of QM are uncoupled from its onerous computational burden.
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Dittner M, Müller J, Aktulga HM, Hartke B. Efficient global optimization of reactive force-field parameters. J Comput Chem 2015; 36:1550-61. [DOI: 10.1002/jcc.23966] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/09/2015] [Accepted: 05/15/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry, Christian-Albrechts-University; Olshausenstr. 40 24098 Kiel Germany
| | - Julian Müller
- Institute for Physical Chemistry, Christian-Albrechts-University; Olshausenstr. 40 24098 Kiel Germany
| | - Hasan Metin Aktulga
- Department of Computer Science and Engineering; Michigan State University; East Lansing Michigan 48824
- Computational Research Division; Lawrence Berkeley National Laboratory; Berkeley California 94720
| | - Bernd Hartke
- Institute for Physical Chemistry, Christian-Albrechts-University; Olshausenstr. 40 24098 Kiel Germany
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42
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Naserifar S, Goddard WA, Tsotsis TT, Sahimi M. First principles-based multiparadigm, multiscale strategy for simulating complex materials processes with applications to amorphous SiC films. J Chem Phys 2015; 142:174703. [DOI: 10.1063/1.4919797] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Saber Naserifar
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | - Theodore T. Tsotsis
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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de Buyl P, Nies E. A parallel algorithm for step- and chain-growth polymerization in molecular dynamics. J Chem Phys 2015; 142:134102. [DOI: 10.1063/1.4916313] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pierre de Buyl
- Division of Polymer Chemistry, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
- SIM vzw, Technologiepark 935, BE-9052 Zwijnaarde, Belgium
| | - Erik Nies
- Division of Polymer Chemistry, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
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Abstract
Combining QMDFF with EVB allows to generate reactive force fields of useful quality for widely varying reactions with minimal effort.
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Affiliation(s)
- Bernd Hartke
- Institute for Physical Chemistry
- Christian-Albrechts-University
- D-24118 Kiel
- Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- Institut für Physikalische und Theoretische Chemie
- Universität Bonn
- 53115 Bonn
- Germany
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45
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Zhang Z, Wang L, Wang Z, He X, Chen Y, Müller-Plathe F, Böhm MC. A coarse-grained molecular dynamics – reactive Monte Carlo approach to simulate hyperbranched polycondensation. RSC Adv 2014. [DOI: 10.1039/c4ra10271a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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46
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Tian Z, Wen J, Ma J. Dynamic simulations of stimuli-responsive switching of azobenzene derivatives in self-assembled monolayers: reactive rotation potential and switching functions. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.918974] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Nagy T, Yosa Reyes J, Meuwly M. Multisurface Adiabatic Reactive Molecular Dynamics. J Chem Theory Comput 2014; 10:1366-75. [PMID: 26580356 DOI: 10.1021/ct400953f] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations.
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Affiliation(s)
- Tibor Nagy
- Department of Chemistry, University of Basel , 4056 Basel, Switzerland
| | | | - Markus Meuwly
- Department of Chemistry, University of Basel , 4056 Basel, Switzerland
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48
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Gamallo P, Prats H, Sayós R. ReaxFF molecular dynamics simulations of CO collisions on an O-preadsorbed silica surface. J Mol Model 2014; 20:2160. [PMID: 24633769 DOI: 10.1007/s00894-014-2160-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/27/2014] [Indexed: 11/28/2022]
Abstract
A quasiclassical trajectory dynamics study was performed for carbon monoxide collisions over an oxygen preadsorbed β-cristobalite (001) surface. A reactive molecular force field (ReaxFF) was used to model the potential energy surface. The collisions were performed fixing several initial conditions: CO rovibrational states (v = 0-5 and j = 0, 20, 35), collision energies (0.05 ≤ E(col) ≤ 2.5 eV), incident angles (θ(v) = 0°, 45°) and surface temperatures (T(surf) = 300 K, 900 K). The principal elementary processes were the molecular reflection and the non-dissociative molecular adsorption. CO₂ molecules were also formed in minor extension via an Eley-Rideal reaction although some of them were finally retained on the surface. The scattered CO molecules tend to be translationally colder and internally hotter (rotationally and vibrationally) than the initial ones. The present study supports that CO + O(ad) reaction should be less important than O + O(ad) reaction over silica for similar initial conditions of reactants, in agreement with experimental data.
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Affiliation(s)
- Pablo Gamallo
- Departament de Química Física and Institut de Química Teòrica i Computacional (IQTC-UB), University of Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
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49
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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50
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Tian Z, Wen J, Ma J. Reactive molecular dynamics simulations of switching processes of azobenzene-based monolayer on surface. J Chem Phys 2013; 139:014706. [DOI: 10.1063/1.4812379] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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