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 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 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>

Anisotropy of Nanoindentation – a tool for the determination of nanocrystal orientation ?

2003 ◽  
Vol 779 ◽  
Author(s):  
David Christopher ◽  
Steven Kenny ◽  
Roger Smith ◽  
Asta Richter ◽  
Bodo Wolf ◽  
...  
Keyword(s):  
Crystal Surface ◽  
Scanning Force Microscopy ◽  
Depth Range ◽  
Dislocation Loops ◽  
Force Microscopy ◽  
Pile Up ◽  
Out Of Plane ◽  
Scanning Force ◽  
Dynamics Simulations

AbstractThe pile up patterns arising in nanoindentation are shown to be indicative of the sample crystal symmetry. To explain and interpret these patterns, complementary molecular dynamics simulations and experiments have been performed to determine the atomistic mechanisms of the nanoindentation process in single crystal Fe{110}. The simulations show that dislocation loops start from the tip and end on the crystal surface propagating outwards along the four in-plane <111> directions. These loops carry material away from the indenter and form bumps on the surface along these directions separated from the piled-up material around the indenter hole. Atoms also move in the two out-of-plane <111> directions causing propagation of subsurface defects and pile-up around the hole. This finding is confirmed by scanning force microscopy mapping of the imprint, the piling-up pattern proving a suitable indicator of the surface crystallography. Experimental force-depth curves over the depth range of a few nanometers do not appear smooth and show distinct pop-ins. On the sub-nanometer scale these pop-ins are also visible in the simulation curves and occur as a result of the initiation of the dislocation loops from the tip.

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>

Modeling the Effects of O-sulfonation on the CID of Serine

2020 ◽  
Author(s):  
Kenneth Lucas ◽  
George Barnes
Keyword(s):  
Sulfo Group ◽  
High Energy ◽  
Empirical Method ◽  
Side Chain ◽  
Energy Structure ◽  
Direct Dynamics ◽  
Theoretical Mass ◽  
Intermolecular Proton Transfer ◽  
Dynamics Simulations ◽  
Semi Empirical

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of \textit{O}-sulfonation on the collision induced dissociation for serine. Towards this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m\z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m\z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The \mz 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also seen that the RM1 semi empirical method was not able to obtain all of the major peaks seen in experiment for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

scholarly journals Gating Competence of Constitutively Open CLC-0 Mutants Revealed by the Interaction with a Small Organic Inhibitor

2003 ◽  
Vol 122 (3) ◽  
pp. 295-306 ◽  
Author(s):  
Sonia Traverso ◽  
Laura Elia ◽  
Michael Pusch
Keyword(s):  
Chloride Channels ◽  
Bound State ◽  
Side Chain ◽  
Pore Channel ◽  
Kinetic Properties ◽  
Wild Type ◽  
High Affinity ◽  
Critical Residue ◽  
Fast Gating

Opening of CLC chloride channels is coupled to the translocation of the permeant anion. From the recent structure determination of bacterial CLC proteins in the closed and open configuration, a glutamate residue was hypothesized to form part of the Cl−-sensitive gate. The negatively charged side-chain of the glutamate was suggested to occlude the permeation pathway in the closed state, while opening of a single protopore of the double-pore channel would reflect mainly a movement of this side-chain toward the extracellular pore vestibule, with little rearrangement of the rest of the channel. Here we show that mutating this critical residue (Glu166) in the prototype Torpedo CLC-0 to alanine, serine, or lysine leads to constitutively open channels, whereas a mutation to aspartate strongly slowed down opening. Furthermore, we investigated the interaction of the small organic channel blocker p-chlorophenoxy-acetic acid (CPA) with the mutants E166A and E166S. Both mutants were strongly inhibited by CPA at negative voltages with a &gt;200-fold larger affinity than for wild-type CLC-0 (apparent KD at −140 mV ∼4 μM). A three-state linear model with an open state, a low-affinity and a high-affinity CPA-bound state can quantitatively describe steady-state and kinetic properties of the CPA block. The parameters of the model and additional mutagenesis suggest that the high-affinity CPA-bound state is similar to the closed configuration of the protopore gate of wild-type CLC-0. In the E166A mutant the glutamate side chain that occludes the permeation pathway is absent. Thus, if gating consists only in movement of this side-chain the mutant E166A should not be able to assume a closed conformation. It may thus be that fast gating in CLC-0 is more complex than anticipated from the bacterial structures.

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