Development of the ChIMES Force Field for Reactive Molecular Systems: Carbon Monoxide at Extreme Conditions

2019 ◽  
Author(s):  
Rebecca Lindsey ◽  
Nir Goldman ◽  
Laurence E. Fried ◽  
Sorin Bastea
Keyword(s):  
Carbon Monoxide ◽  
Molecular System ◽  
Interaction Model ◽  
System Size ◽  
Single Atom ◽  
Reactive System ◽  
Extreme Conditions ◽  
Ambient Conditions ◽  
Molecular Systems ◽  
Three Body

<p>The interatomic Chebyshev Interaction Model for Efficient Simulation (ChIMES) is based on linear combinations of Chebyshev polynomials describing explicit two- and three-body interactions. Recently, the ChIMES model has been developed and applied to a molten metallic system of a single atom type (carbon), as well as a non-reactive molecular system of two atom types at ambient conditions (water). Here, we continue application of ChIMES to increasingly complex problems through extension to a reactive system. Specifically, we develop a ChIMES model for carbon monoxide under extreme conditions, with built-in transferability to nearby state points. We demonstrate that the resulting model recovers much of the accuracy of DFT while exhibiting a 10<sup>4</sup>increase in efficiency, linear system size scalability and the ability to overcome the significant system size effects exhibited by DFT.</p>

Development of the ChIMES Force Field for Reactive Molecular Systems: Carbon Monoxide at Extreme Conditions

2019 ◽  
Author(s):  
Rebecca Lindsey ◽  
Nir Goldman ◽  
Laurence E. Fried ◽  
Sorin Bastea
Keyword(s):  
Force Field ◽  
Cluster Formation ◽  
Extreme Temperature ◽  
Interaction Model ◽  
System Size ◽  
Quantum Molecular Dynamics ◽  
Many Body ◽  
Molecular Systems ◽  
Molecular Dynamics Methods ◽  
The Many

<p>We have developed a transferable reactive force field for C/O systems under extreme temperature and pressure conditions based on the many-body Chebyshev Interaction Model for Efficient Simulation (ChIMES). The resulting model is shown to recover much of the accuracy of DFT for prediction of structure, dynamics and chemistry when applied to dissociative systems at 1:1 and 1:2 C:O ratios, as well as molten carbon. Our C/O modeling approach exhibits a 10<sup>4</sup> increase in efficiency and linear system size scalability over standard quantum molecular dynamics methods, allowing simulation of significantly larger systems than previously possible. Furthermore, we show that system sizes of at least 500 atoms are required to observe the formation of experimentally predicted molten carbon condensates under oxygen-deficient conditions, indicative of possible system size effects in quantum simulations of these types of systems. Overall, we find the present ChIMES model to be well suited for modeling chemical processes and cluster formation at pressures and temperatures typical of shock waves. We expect that the present C/O modeling paradigm can serve as a template for the development of a high pressure --high temperature organic chemistry force-field. </p>

scholarly journals Resolving sub-angstrom ambient motion through reconstruction from vibrational spectra

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jack Griffiths ◽  
Tamás Földes ◽  
Bart de Nijs ◽  
Rohit Chikkaraddy ◽  
Demelza Wright ◽  
...  
Keyword(s):  
Single Molecule ◽  
Imaging Techniques ◽  
Surface Enhanced Raman Spectroscopy ◽  
Atomic Scale ◽  
Single Atom ◽  
Ambient Conditions ◽  
Molecular Systems ◽  
Surface Enhanced Raman ◽  
Metal Organic ◽  
Molecule Interactions

AbstractMetal/organic-molecule interactions underpin many key chemistries but occur on sub-nm scales where nanoscale visualisation techniques tend to average over heterogeneous distributions. Single molecule imaging techniques at the atomic scale have found it challenging to track chemical behaviour under ambient conditions. Surface-enhanced Raman spectroscopy can optically monitor the vibrations of single molecules but understanding is limited by the complexity of spectra and mismatch between theory and experiment. We demonstrate that spectra from an optically generated metallic adatom near a molecule of interest can be inverted into dynamic sub-Å metal-molecule interactions using a comprehensive model, revealing anomalous diffusion of a single atom. Transient metal-organic coordination bonds chemically perturb molecular functional groups > 10 bonds away. With continuous improvements in computational methods for modelling large and complex molecular systems, this technique will become increasingly applicable to accurately tracking more complex chemistries.

Development of the ChIMES Force Field for Reactive Molecular Systems: Carbon Monoxide at Extreme Conditions

2019 ◽  
Author(s):  
Rebecca Lindsey ◽  
Nir Goldman ◽  
Laurence E. Fried ◽  
Sorin Bastea
Keyword(s):  
Force Field ◽  
Cluster Formation ◽  
Extreme Temperature ◽  
Interaction Model ◽  
System Size ◽  
Quantum Molecular Dynamics ◽  
Many Body ◽  
Molecular Systems ◽  
Molecular Dynamics Methods ◽  
The Many

<p>We have developed a transferable reactive force field for C/O systems under extreme temperature and pressure conditions based on the many-body Chebyshev Interaction Model for Efficient Simulation (ChIMES). The resulting model is shown to recover much of the accuracy of DFT for prediction of structure, dynamics and chemistry when applied to dissociative systems at 1:1 and 1:2 C:O ratios, as well as molten carbon. Our C/O modeling approach exhibits a 10<sup>4</sup> increase in efficiency and linear system size scalability over standard quantum molecular dynamics methods, allowing simulation of significantly larger systems than previously possible. Furthermore, we show that system sizes of at least 500 atoms are required to observe the formation of experimentally predicted molten carbon condensates under oxygen-deficient conditions, indicative of possible system size effects in quantum simulations of these types of systems. Overall, we find the present ChIMES model to be well suited for modeling chemical processes and cluster formation at pressures and temperatures typical of shock waves. We expect that the present C/O modeling paradigm can serve as a template for the development of a high pressure --high temperature organic chemistry force-field. </p>

The initial reaction mechanism and thermal sensitivity of a fluoropolymer-containing energetic molecular system: the coupling effect of interfacial interactions and free radical reactions

CrystEngComm ◽  
2021 ◽  
Vol 23 (16) ◽  
pp. 3006-3014
Author(s):  
Wen Qian
Keyword(s):  
Free Radical ◽  
Coupling Effect ◽  
Molecular System ◽  
Thermal Sensitivity ◽  
Radical Reactions ◽  
Initial Reaction ◽  
Interfacial Interactions ◽  
Free Radical Reactions ◽  
Molecular Systems ◽  
Reactive Molecular Dynamics

A strategy combining classic and reactive molecular dynamics is applied to find the coupling effect of interfacial interactions and free radical reactions during the initial thermal decomposition of fluoropolymer-containing molecular systems.

NO, CO and H2S based pharmaceuticals in the mission of vision (eye health): a comprehensive review

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Jan Mohammad Mir ◽  
Ram Charitra Maurya ◽  
Mohd Washid Khan
Keyword(s):  
Nitric Oxide ◽  
Carbon Monoxide ◽  
Human Physiology ◽  
Hydrogen Sulfide ◽  
The Other ◽  
Normal Functioning ◽  
Comprehensive Review ◽  
Molecular Systems ◽  
Eye Health ◽  
Highly Sensitive

Abstract A set of well defined signaling molecules responsible for normal functioning of human physiology including nitric oxide along with carbon monoxide and hydrogen sulphide are referred as “gasotransmitters”. Due to their involvement in almost every system of a human body, the care of highly sensitive organs using these molecules as drugs represents highly fascinating area of research. In connection with these interesting aspects, the applied aspects of these gaseous molecules in maintaining healthy eye and vision have been targeted in this review. Several examples of eye-droppers including NORMs like latanoprost and nipradiol, CORMs like CORM-3 and CORM-A1, and Hydrogen sulfide releasing system like GYY4137 have been discussed in this context. Therefore the relation of these trio-gasotransmitters with the ophthalmic homeostasis on one hand, and de-infecting role on the other hand has been mainly highlighted. Some molecular systems capable of mimicking gasotransmitter action have also been introduced in connection with the titled theme.

Design and Off-Design Analysis of a MW Hybrid System Based on Rolls-Royce Integrated Planar Solid Oxide Fuel Cells

2007 ◽  
Vol 129 (3) ◽  
pp. 792-797 ◽  
Author(s):  
Loredana Magistri ◽  
Michele Bozzolo ◽  
Olivier Tarnowski ◽  
Gerry Agnew ◽  
Aristide F. Massardo
Keyword(s):  
Fuel Cells ◽  
Solid Oxide Fuel Cells ◽  
Hybrid System ◽  
System Size ◽  
Solid Oxide ◽  
Oxide Fuel ◽  
Ambient Conditions ◽  
Detailed Model ◽  
Design Point ◽  
Turbine Speed

In this paper the design point definition of a pressurised hybrid system based on the Rolls-Royce Integrated Planar-Solid Oxide Fuel Cells (IP-SOFCs) is presented and discussed. The hybrid system size is about 2 MWe and the design point analysis has been carried out using two different IP-SOFC models developed by Thermochemical Power Group (TPG) at the University of Genoa: (i) a generic one, where the transport and balance equations of the mass, energy and electrical charges are solved in a lumped volume at constant temperature; (ii) a detailed model where all the equations are solved in a finite difference approach inside the single cell. The first model has been used to define the hybrid system lay out and the characteristics of the main devices of the plant such as the recuperator, the compressor, the expander, etc. The second model has been used to verify the design point defined in the previous step, taking into account that the stack internal temperature behavior are now available and must be carefully considered. Apt modifications of the preliminary design point have been suggested using the detailed IP-SOFC system to obtain a feasible solution. In the second part of the paper some off-design performance of the Hybrid System carried out using detailed SOFC model are presented and discussed. In particular the influence of ambient conditions is shown, together with the possible part load operations at fixed and variable gas turbine speed. Some considerations on the compressor surge margin modification are reported.

Graph theory approach

1983 ◽  
Vol 48 (8) ◽  
pp. 2097-2117 ◽  
Author(s):  
Vladimír Kvasnička
Keyword(s):  
Organic Chemistry ◽  
Computer Simulation ◽  
Graph Theory ◽  
Chemical Reaction ◽  
Molecular System ◽  
Theory Approach ◽  
Molecular Systems

A graph-theory formalism of the organic chemistry is suggested. The molecular system is considered as a multigraph with loops, the vertices are evaluated by their mapping onto the vocabulary of vertex labels (e.g. atomic symbols). A multiedge of multiplicity t corresponds to a t-tuple (single, double, triple, etc) bond. The chemical reaction of molecular systems is treated by the transformation of graphs. The suggested graph-theory approach allows to formalize many notions and concepts that are naturally emerging in the computer simulation of organic chemistry.

scholarly journals Dynamic Graphical Models of Molecular Kinetics

2018 ◽  
Author(s):  
Simon Olsson ◽  
Frank Noé
Keyword(s):  
Graphical Models ◽  
Molecular System ◽  
System Size ◽  
Ising Models ◽  
Metastable States ◽  
Dynamics Simulation ◽  
Global State ◽  
Stable States ◽  
Markov State ◽  
State Models

AbstractMost current molecular dynamics simulation and analysis methods rely on the idea that the molecular system can be characterized by a single global state, e.g., a Markov State in a Markov State Model (MSM). In this approach, molecules can be extensively sampled and analyzed when they only possess a few metastable states, such as small to medium-sized proteins. However this approach breaks down in frustrated systems and in large protein assemblies, where the number of global meta-stable states may grow exponentially with the system size. Here, we introduce Dynamic Graphical Models (DGMs), which build upon the idea of Ising models, and describe molecules as assemblies of coupled subsystems. The switching of each sub-system state is only governed by the states of itself and its neighbors. DGMs need many fewer parameters than MSMs or other global-state models, in particular we do not need to observe all global system configurations to estimate them. Therefore, DGMs can predict new, previously unobserved, molecular configurations. Here, we demonstrate that DGMs can faithfully describe molecular thermodynamics and kinetics and predict previously unobserved metastable states for Ising models and protein simulations.

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