scholarly journals Collisional Dynamics Simulations Revealing Fragmentation Properties of Zn(II)-Bound Poly-Peptide

2020 ◽  
Author(s):  
Abdul Malik ◽  
Laurence A. Angel ◽  
Riccardo Spezia ◽  
William L. Hase
Keyword(s):  
Collision Energy ◽  
Activation Barrier ◽  
Probability Distributions ◽  
Fragmentation Pathways ◽  
Reactive Trajectories ◽  
Collisional Dynamics ◽  
Direct Collision ◽  
Dynamics Simulations ◽  
Thermal Simulations ◽  
Collision Energy Transfer

<div> <div> <div> <p>Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc binding on reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal/mol which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal/mol identified previously during thermal simulations. This difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with the Ar projectile. </p> </div> </div> </div>

scholarly journals Collisional Dynamics Simulations Revealing Fragmentation Properties of Zn(II)-Bound Poly-Peptide

2020 ◽  
Author(s):  
Abdul Malik ◽  
Laurence A. Angel ◽  
Riccardo Spezia ◽  
William L. Hase
Keyword(s):  
Collision Energy ◽  
Activation Barrier ◽  
Probability Distributions ◽  
Fragmentation Pathways ◽  
Reactive Trajectories ◽  
Collisional Dynamics ◽  
Direct Collision ◽  
Dynamics Simulations ◽  
Thermal Simulations ◽  
Collision Energy Transfer

<div> <div> <div> <p>Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analogue methanobactin peptide-5, amb5) and in particular to explore the role of zinc binding on reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal/mol which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal/mol identified previously during thermal simulations. This difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with the Ar projectile. </p> </div> </div> </div>

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

scholarly journals Effects of temperatures on pressure-induced structural changes in amorphous Si: A molecular-dynamics study

10.29007/6kp3 ◽  
2020 ◽  
Author(s):  
Renji Mukuno ◽  
Manabu Ishimaru
Keyword(s):  
Molecular Dynamics ◽  
Phase Transformation ◽  
Amorphous Phase ◽  
Structural Changes ◽  
Interatomic Potential ◽  
Activation Barrier ◽  
Distribution Functions ◽  
High Density ◽  
Angle Distribution ◽  
Dynamics Simulations

The structural changes of amorphous silicon (a-Si) under compressive pressure were examined by molecular-dynamics simulations using the Tersoff interatomic potential. a-Si prepared by melt-quenching methods was pressurized up to 30 GPa under different temperatures (300K and 500K). The density of a-Si increased from 2.26 to 3.24 g/cm3 with pressure, suggesting the occurrence of the low-density to high-density amorphous phase transformation. This phase transformation occurred at the lower pressure with increasing the temperature because the activation barrier for amorphous-to-amorphous phase transformation could be exceeded by thermal energy. The coordination number increased with pressure and time, and it was saturated at different values depending on the pressure. This suggested the existence of different metastable atomic configurations in a-Si. Atomic pair-distribution functions and bond-angle distribution functions suggested that the short-range ordered structure of high-density a-Si is similar to the structure of the high-pressure phase of crystalline Si (β-tin and Imma structures).

The Role of SiH3 Diffusion in Determining the Surface Smoothness of Plasma-Deposited Amorphous Si Thin Films: An Atomic-Scale Analysis

2005 ◽  
Vol 862 ◽  
Author(s):  
Mayur S. Valipa ◽  
Tamas Bakos ◽  
Eray S. Aydil ◽  
Dimitrios Maroudas
Keyword(s):  
Thin Films ◽  
Density Functional ◽  
Activation Barrier ◽  
Density Functional Theory Calculations ◽  
Atomic Scale ◽  
Functional Theory ◽  
Weak Adsorption ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous

AbstractDevice-quality hydrogenated amorphous silicon (a-Si:H) thin films grown under conditions where the SiH3 radical is the dominant deposition precursor are remarkably smooth, as the SiH3 radical is very mobile and fills surface valleys during its diffusion on the a-Si:H surface. In this paper, we analyze atomic-scale mechanisms of SiH3 diffusion on a-Si:H surfaces based on molecular-dynamics simulations of SiH3 radical impingement on surfaces of a-Si:H films. The computed average activation barrier for radical diffusion on a-Si:H is 0.16 eV. This low barrier is due to the weak adsorption of the radical onto the a-Si:H surface and its migration predominantly through overcoordination defects; this is consistent with our density functional theory calculations on crystalline Si surfaces. The diffusing SiH3 radical incorporates preferentially into valleys on the a-Si:H surface when it transfers an H atom and forms a Si-Si backbond, even in the absence of dangling bonds.

Molecular Dynamics Simulations of Hypervelocity Buckminsterfullerene Collisions

1994 ◽  
Vol 359 ◽  
Author(s):  
D.H. Robertson ◽  
D.W. Brenner ◽  
C.T. White
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Collision Energy ◽  
Center Of Mass ◽  
High Energy ◽  
Translational Energy ◽  
Inelastic Behavior ◽  
Fusion Probability ◽  
High Energy Collisions ◽  
Dynamics Simulations

ABSTRACTMolecular dynamics simulations of high-energy collisions between various combinations of C60 and C70 fullerenes were performed to calculate the threshold for molecular fusion of these clusters as a function of the center-of-mass collision energy. For collision energies below 90 eV, only non-reacting collisions occurred with no observation of any fusion. However, at higher collision energies molecular fusion of the colliding clusters was observed with the fusion probability approaching 1 by 160 eV collision energy. The non-fusing, rebounding collisions showed deeply inelastic behavior with the loss of translational energy to internal energy varying from 50 to 70 percent.

scholarly journals Determination of Kinetic Properties in Unimolecular Dissociation of Complex Systems from Graph-Theory Based Analysis of an Ensemble of Reactive Trajectories.

2021 ◽  
Author(s):  
Ariel F. Perez-Mellor ◽  
Riccardo Spezia
Keyword(s):  
Graph Theory ◽  
Complex Systems ◽  
Kinetic Properties ◽  
Unimolecular Dissociation ◽  
Theoretical Mass ◽  
Reactive Trajectories ◽  
Direct Counting ◽  
Dynamics Simulations ◽  
State Kinetic

<div>We describe and apply a general approach based on graph-theory to obtain kinetic and structural properties from direct dynamics simulations. In particular, we focus on the unimolecular fragmentation of complex systems in which, prior to dissociation, different events can take place, and notably isomerizations and formation of ion-molecule complex.</div><div>3-state and 4-state kinetic models are thus obtained and rate constants for global or specific pathways are obtained from direct counting and flux calculation, both being in agreement.<br />Finally, we show how a theoretical mass spectrum can also be obtained automatically.<br /></div>

scholarly journals Extended Peptide Basis Set for Variational Markov Models: Secondary Structure, Orthonormality, and Undersampled Transitions

2018 ◽  
Author(s):  
Louis Martini ◽  
Bettina Keller
Keyword(s):  
Markov Models ◽  
Probability Distributions ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Peptide Sequence ◽  
Basis Set ◽  
Variational Models ◽  
Helix Formation ◽  
Α Helix ◽  
Dynamics Simulations

<div><div><div><p>The variational approach to conformational dynamics offers a systematic way to con- struct kinetic models from molecular dynamics simulations, using an arbitrary set of basis functions. We have recently proposed a basis set for peptide systems that only depends on the sequence of amino acids in the system. This basis set is not data- driven and can therefore be used to compare models for different MD simulations. Here we introduce an orthonormality condition for this basis set as a requirement for the variational models to remain directly interpretable. The orthonormality condi- tion naturally leads to a way of detecting correlations between the sampled marginal stationary probability distributions at each residue in the peptide sequence. We show how these correlations emerge from either undersampled transitions or from inher- ent dynamical dependencies between the residues. Our basis set relies on a tensor structure obtained from residue-centered ansatz functions. We demonstrate that this structure is sufficient to model both β-sheet and α-helix formation in peptides.</p></div></div></div>

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