Molecular dynamics effects on luminescence properties of oligothiophene derivatives: a molecular mechanics–response theory study based on the CHARMM force field and density functional theory

2011 ◽  
Vol 13 (39) ◽  
pp. 17532 ◽  
Author(s):  
Jonas Sjöqvist ◽  
Mathieu Linares ◽  
Mikael Lindgren ◽  
Patrick Norman
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Force Field ◽  
Molecular Mechanics ◽  
Density Functional ◽  
Luminescence Properties ◽  
Response Theory ◽  
Functional Theory ◽  
Charmm Force Field

scholarly journals Calculation of the Detonation State of HN3 with Quantum Accuracy

2020 ◽  
Author(s):  
Cong Huy Pham ◽  
Rebecca Lindsey ◽  
Laurence E. Fried ◽  
Nir Goldman
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Potential Energy ◽  
Force Field ◽  
Density Functional ◽  
Energy Surface ◽  
Detonation Properties ◽  
Training Set ◽  
Functional Theory ◽  
Wide Range

<div>HN<sub>3</sub> is a unique liquid energetic material that exhibits ultrafast detonation chemistry and a transition to metallic states during detonation. We combine the ChIMES many-body reactive force field and the extended-Lagrangian multiscale shock technique (MSST) molecular dynamics method to calculate the detonation properties of HN<sub>3</sub> with the accuracy of Kohn-Sham density-functional theory. ChIMES is based on a Chebyshev polynomial expansion and can accurately reproduce density-functional theory molecular dynamics (DFT-MD) simulations for a wide range of unreactive and decomposition conditions of liquid HN<sub>3</sub>. We show that addition of random displacement configurations and the energies of gas-phase equilibrium products in the training set allows ChIMES to efficiently explore the complex potential energy surface. Schemes for selecting force field parameters and the inclusion of stress tensor and energy data in the training set are examined. Structural and dynamical properties, as well as chemistry predictions for the resulting models are benchmarked against DFT-MD. We demonstrate that the inclusion of explicit four-body energy terms is necessary to capture the potential energy surface across a wide range of conditions. The present force field, which was fit to a balance of forces, energies, and stress tensors yields excellent agreement with DFT, while exhibiting an orders-of-magnitude increase in computational efficiency over DFT-MD. Our results generally retain the accuracy of DFT-MD while yielding a high degree of computational efficiency, allowing simulations to approach orders of magnitude larger time and spatial scales. The techniques and recipes for MD model creation we present allow for direct simulation of nanosecond shock compression experiments and calculation of the detonation properties of materials with the accuracy of Kohn-Sham density-functional theory.</div>

scholarly journals Teaching Enzyme Catalysis Using an Open Source Framework for Interactive Molecular Dynamics in Virtual Reality

2019 ◽  
Author(s):  
Simon Bennie ◽  
Kara Ranaghan ◽  
Helen Deeks ◽  
Heather Goldsmith ◽  
Mike O'Connor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Virtual Reality ◽  
Open Source ◽  
Molecular Mechanics ◽  
Real Time ◽  
Density Functional ◽  
Traditional Approach ◽  
Chorismate Mutase ◽  
Functional Theory

<div> <div> <p>The reemergence of virtual reality (VR) in the last few years has led to affordable commodity hardware that can offer new ways to teach, communicate and engage with difficult concepts, especially those which involve complicated 3D motion and spatial manipulation. In a higher education context, these immersive technologies make it possible to teach complex molecular topics in a way that may aid or even supersede traditional approaches such as molecular models, textbook images, and traditional screen-based computational environments. In this work we describe a study involving 24 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class complemented with an additional component utilising real-time interactive molecular dynamics simulations in VR (iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described,(1) and building on recent work where we demonstrated the ability to use this framework to run ‘on-the-fly’ density functional theory in VR at interactive speeds,2 we designed three tasks for students to complete in iMD-VR: (1) interactive rearrangement of the chorismate molecule to prephenate using forces obtained from ‘on-the-fly’ density functional theory calculations; (2) unbinding of chorismate from the active site chorismate mutase enzyme using molecular-mechanics forces calculated in real-time; and (3) docking of chorismate with chorismate mutase using real-time molecular mechanics forces. A survey indicated that most students found the iMD-VR component more engaging than the traditional approach, and also that it improved their perceived educational outcomes and their interest in continuing on in the field of computational sciences. </p></div> </div>

scholarly journals Teaching Enzyme Catalysis Using an Open Source Framework for Interactive Molecular Dynamics in Virtual Reality

2019 ◽  
Author(s):  
Simon Bennie ◽  
Kara Ranaghan ◽  
Helen Deeks ◽  
Heather Goldsmith ◽  
Mike O'Connor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Virtual Reality ◽  
Open Source ◽  
Molecular Mechanics ◽  
Real Time ◽  
Density Functional ◽  
Traditional Approach ◽  
Chorismate Mutase ◽  
Functional Theory

<div> <div> <p>The reemergence of virtual reality (VR) in the last few years has led to affordable commodity hardware that can offer new ways to teach, communicate and engage with difficult concepts, especially those which involve complicated 3D motion and spatial manipulation. In a higher education context, these immersive technologies make it possible to teach complex molecular topics in a way that may aid or even supersede traditional approaches such as molecular models, textbook images, and traditional screen-based computational environments. In this work we describe a study involving 24 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class complemented with an additional component utilising real-time interactive molecular dynamics simulations in VR (iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described,(1) and building on recent work where we demonstrated the ability to use this framework to run ‘on-the-fly’ density functional theory in VR at interactive speeds,2 we designed three tasks for students to complete in iMD-VR: (1) interactive rearrangement of the chorismate molecule to prephenate using forces obtained from ‘on-the-fly’ density functional theory calculations; (2) unbinding of chorismate from the active site chorismate mutase enzyme using molecular-mechanics forces calculated in real-time; and (3) docking of chorismate with chorismate mutase using real-time molecular mechanics forces. A survey indicated that most students found the iMD-VR component more engaging than the traditional approach, and also that it improved their perceived educational outcomes and their interest in continuing on in the field of computational sciences. </p></div> </div>

scholarly journals Calculation of the Detonation State of HN3 with Quantum Accuracy

2020 ◽  
Author(s):  
Cong Huy Pham ◽  
Rebecca Lindsey ◽  
Laurence E. Fried ◽  
Nir Goldman
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Potential Energy ◽  
Force Field ◽  
Density Functional ◽  
Energy Surface ◽  
Detonation Properties ◽  
Training Set ◽  
Functional Theory ◽  
Wide Range

<div>HN<sub>3</sub> is a unique liquid energetic material that exhibits ultrafast detonation chemistry and a transition to metallic states during detonation. We combine the ChIMES many-body reactive force field and the extended-Lagrangian multiscale shock technique (MSST) molecular dynamics method to calculate the detonation properties of HN<sub>3</sub> with the accuracy of Kohn-Sham density-functional theory. ChIMES is based on a Chebyshev polynomial expansion and can accurately reproduce density-functional theory molecular dynamics (DFT-MD) simulations for a wide range of unreactive and decomposition conditions of liquid HN<sub>3</sub>. We show that addition of random displacement configurations and the energies of gas-phase equilibrium products in the training set allows ChIMES to efficiently explore the complex potential energy surface. Schemes for selecting force field parameters and the inclusion of stress tensor and energy data in the training set are examined. Structural and dynamical properties, as well as chemistry predictions for the resulting models are benchmarked against DFT-MD. We demonstrate that the inclusion of explicit four-body energy terms is necessary to capture the potential energy surface across a wide range of conditions. The present force field, which was fit to a balance of forces, energies, and stress tensors yields excellent agreement with DFT, while exhibiting an orders-of-magnitude increase in computational efficiency over DFT-MD. Our results generally retain the accuracy of DFT-MD while yielding a high degree of computational efficiency, allowing simulations to approach orders of magnitude larger time and spatial scales. The techniques and recipes for MD model creation we present allow for direct simulation of nanosecond shock compression experiments and calculation of the detonation properties of materials with the accuracy of Kohn-Sham density-functional theory.</div>

Excited state Born–Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA

2020 ◽  
Vol 22 (35) ◽  
pp. 19532-19541
Author(s):  
Michele Nottoli ◽  
Benedetta Mennucci ◽  
Filippo Lipparini
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Excited State ◽  
Force Field ◽  
Density Functional ◽  
Time Dependent ◽  
Functional Theory ◽  
Amoeba Force Field ◽  
Dependent Density

We present the implementation of excited state Born–Oppenheimer molecular dynamics (BOMD) using a polarizable QM/MM approach based on time-dependent density functional theory (TDDFT) formulation and the AMOEBA force field.

scholarly journals Dietary polyphenols mitigate SARS-CoV-2 main protease (Mpro) – Molecular Dynamics, Molecular Mechanics, and Density Functional Theory Investigations.

2021 ◽  
pp. 131879
Author(s):  
Temitope Isaac Adelusi ◽  
Abdul-Quddus Kehinde Oyedele ◽  
Ojo Emmanuel Monday ◽  
Ibrahim Damilare Boyenle ◽  
Mukhtar Oluwaseun Idris ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Molecular Mechanics ◽  
Density Functional ◽  
Functional Theory ◽  
Dietary Polyphenols ◽  
Main Protease
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