scholarly journals The IR spectrum of supercritical water: Combined molecular dynamics/quantum mechanics strategy and force field for cluster sampling

2011 ◽  
Vol 112 (13) ◽  
pp. 2578-2584 ◽  
Author(s):  
P. Bordat ◽  
D. Bégué ◽  
R. Brown ◽  
A. Marbeuf ◽  
H. Cardy ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Force Field ◽  
Supercritical Water ◽  
Ir Spectrum ◽  
Cluster Sampling

A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)-block-poly(ε-caprolactone) (PEG-b-PCL) micelles

2020 ◽  
Vol 22 (41) ◽  
pp. 24028-24040
Author(s):  
Maryam S. Sadeghi ◽  
Mohammad Reza Moghbeli ◽  
William A. Goddard
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Force Field ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Coarse Grain ◽  
The Novel ◽  
Poly Ethylene Glycol ◽  
P Application ◽  
Poly Ethylene

Application of the novel quantum based coarse grained force field (CGq FF) for formation of a micelle from 250 chains of 2000 Dalton CG-MePEG23-b-PCL9 block copolymer in water at 310.15 K.

scholarly journals Bioinorganic Membrane Using Kurumi, A New Liquid Crystal

2021 ◽  
pp. 4-7
Author(s):  
Ricardo Gobato ◽  
Alireza Heidari ◽  
Abhijit Mitra
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Liquid Crystal ◽  
Force Field ◽  
Experimental Verification ◽  
Computational Simulation ◽  
Single Layer ◽  
Applied Theory ◽  
Micellar Structure ◽  
Scientific Name

The work characterizes develop a single layer bioinorganic membrane using nano-molecule Kurumi C13H20BeLi2SeSi / C13H19BeLi2SeSi, is well characterize computationally. As its scientific name 3-lithio-3-(6-{3-selena-8-beryllatricyclo [3.2.1.02,⁴] oct-6-en-2-yl}hexyl)-1-sila-2-lithacyclopropane. The work was based on a molecular dynamics (MD) of 1ns, using the CHARMM22 force field, with step 0.001 ps. Calculations indicate that the final structure, arrangement have the tendency to form a single layer micellar structure, when molecular dynamics is performed with a single layer. However, when molecular dynamics were carried out in several layers, indicates the behavior of a liotropic nematic liquid crystal order. Kurumi features the structure polar-apolar-polar predominant. Limitations our study has so far been limited to computational simulation via quantum mechanics e molecular mechanics (QM/MM), an applied theory. Our results and calculations are compatible and with the theory of QM/MM, but their physical experimental verification depend on advanced techniques for their synthesis, obtaining laboratory for experimental biochemical. Going beyond imagination, the most innovative and challenging proposal of the work advances the construction of a structure compatible with the formation of a “new DNA”, based now on the kurumi molecule.

scholarly journals Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics

2021 ◽  
Author(s):  
Mei Zheng ◽  
Andres Jaramillo-Botero ◽  
Xue-hai Ju ◽  
William A. Goddard
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Equation Of State ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Coarse Grained ◽  
Polyacrylamide Gels ◽  
Dynamics Simulations

Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.

scholarly journals Revealing of Supercritical Water Gasification Process of Lignin by Reactive Force Field Molecular Dynamics Simulations

Processes ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 714
Author(s):  
Veerapandian Ponnuchamy ◽  
Jakub Sandak ◽  
Anna Sandak
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Supercritical Water ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Gasification Process ◽  
Lignin Model ◽  
Supercritical Water Gasification ◽  
Dynamics Simulations

Gasification with supercritical water is an efficient process that can be used for the valorization of biomass. Lignin is the second most abundant biopolymer in biomass and its conversion is fundamental for future energy and value-added chemicals. In this paper, the supercritical water gasification process of lignin by employing reactive force field molecular dynamics simulations (ReaxFF MD) was investigated. Guaiacyl glycerol-β-guaiacyl ether (GGE) was considered as a lignin model to evaluate the reaction mechanism and identify the components at different temperatures from 1000 K to 5000 K. The obtained results revealed that the reactions and breaking of the lignin model started at 2000 K. At the primary stage of the reaction at 2000 K the β-O-4 bond tends to break into several compounds, forming mainly guaiacol and 1,3-benzodioxole. In particular, 1,3-benzodioxole undergoes dissociation and forms cyclopentene-based ketones. Afterward, dealkylation reaction occurred through hydroxyl radicals of water to form methanol, formaldehyde and methane. Above 2500 K, H2, CO and CO2 are predominantly formed in which water molecules contributed hydrogen and oxygen for their formation. Understanding the detailed reactive mechanism of lignin’s gasification is important for efficient energy conversion of biomass.

scholarly journals Development of Site-Specific Mg2+–RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

2016 ◽  
Vol 13 (1) ◽  
pp. 340-352 ◽  
Author(s):  
Lorenzo Casalino ◽  
Giulia Palermo ◽  
Nodira Abdurakhmonova ◽  
Ursula Rothlisberger ◽  
Alessandra Magistrato
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Force Field ◽  
Site Specific ◽  
Force Field Parameters

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

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