Dynamical, spectroscopic and computational imaging of bond breaking in photodissociation: roaming and role of conical intersections

2015 ◽  
Vol 177 ◽  
pp. 77-98 ◽  
Author(s):  
Masaaki Nakamura ◽  
Po-Yu Tsai ◽  
Toshio Kasai ◽  
King-Chuen Lin ◽  
Federico Palazzetti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy Surfaces ◽  
Minimum Energy ◽  
Saddle Points ◽  
Integrated Approach ◽  
Computational Imaging ◽  
Ion Imaging ◽  
Structural Investigations ◽  
Alternative Pathways ◽  
Fragmentation Threshold

Recent experimental and theoretical advances in the study of the dissociation of excited molecules are revealing unexpected mechanisms, when their outcomes are tackled by combining (i) space-time ion imaging of translational features, with (ii) spectroscopic probing of rotational and vibrational distributions; crucial is the assistance of (iii) the quantum chemistry of structural investigations of rearrangements of chemical bonds, and of (iv) the simulations of molecular dynamics to follow the evolution of selective bond stretching and breaking. Here we present results of such an integrated approach to methyl formate, HCOOCH3, the simplest of esters; the main focus is on the rotovibrationally excited CO (v = 1) product and in general on the energy distribution in the fragments. Previous laser studies of dissociation into CO and CH3OH at a sequence of various wavelengths discovered signatures of a roaming mechanism by the late arrival of CO (v = 0) products in time-of-flight ion imaging. Subsequent detailed investigations as a function of excitation energy provided the assessment of the threshold, which opens for triple breakdown into CO and further fragments H and CH3O, as spectroscopically characterized by ion imaging and FTIR respectively. Accompanying quantum mechanical electronic structure calculations and classical molecular dynamics simulations clarify the origin of these fragments through “roaming” pathways involving incipient radical intermediates at energies below the triple fragmentation threshold: a specific role is played by nonadiabatic transitions at a conical intersection between ground and excited states; alternative pathways focalize our attention to regions of the potential energy surfaces other than those in the neighbourhoods of saddle points along minimum energy paths: eventually this leads us to look for avenues in reaction kinetics beyond those of venerable transition state theories.

Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

2021 ◽  
Vol 23 (9) ◽  
pp. 5236-5243
Author(s):  
Ying Hu ◽  
Chao Xu ◽  
Linfeng Ye ◽  
Feng Long Gu ◽  
Chaoyuan Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Dynamics Simulation ◽  
Surface Hopping ◽  
Nonadiabatic Molecular Dynamics ◽  
Energy Surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation.

Structural stability of CmTin microclusters and nanoparticles: Molecular–dynamics simulations

2005 ◽  
Vol 1 (4) ◽  
pp. 204-209
Author(s):  
O.B. Malcıoğlu ◽  
Ş. Erkoç
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binary Systems ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Atomic Interactions ◽  
Dynamics Simulations ◽  
Three Body ◽  
Initial Geometry

The minimum energy structures of CmTin microclusters and nanoparticles have been investigated theoretically by performing molecular–dynamics (MD) simulations. Selected crystalline and completely random initial geometries are considered. The potential energy function (PEF) used in the calculations includes two– and three–body atomic interactions for C-Ti binary systems. Molecular–dynamics simulations have been performed at 1 K and 300 K. It has been found that initial geometry has a very strong influence on relaxed geometry

scholarly journals Energetic Self-Folding Mechanism in α-Helixes

2019 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Javier Cerezo
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy Surfaces ◽  
Reasonable Agreement ◽  
Dihedral Angles ◽  
Native Conformation ◽  
Experimental Values ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Energy Surfaces ◽  
Large Peptide

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive Molecular Dynamics simulations. The Energetic Self-Folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues towards the α<sub>R </sub>conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation, or zipper models, and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.

Structural and Mechanical Properties of a Simulated Nickel Nanophase

1995 ◽  
Vol 400 ◽  
Author(s):  
G. D’Agostino ◽  
H. Van Swygenhoven
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Local Minimum ◽  
Minimum Energy ◽  
Perfect Crystal ◽  
Atomic Level ◽  
Dynamic Evolution ◽  
Plastic Behaviour ◽  
Simulated Sample ◽  
Parallel Code

AbstractThe present paper is aimed at studying the physics of a nickel nanophase at the atomic level. A dense polycrystal has been designed by ideally growing many nano-crystals from randomly distributed seeds and truncating them through a Voronoi construction. The sample has been brought to thermodynamic equilibrium and quenched to its local minimum energy thus leading to a mechanically stable system. The dynamic evolution has been simulated by means of classical molecular dynamics employing a Finnis-Sinclair interactive potential. Owing to the large number of atoms required, a parallel code has been developed. Elastic and plastic behaviour of the simulated sample has been compared with that of a perfect crystal. Evidence of an enhanced plastic behaviour has been observed when severe tensile stresses are applied.

Towards a Virtual Laboratory for Grain Boundaries and Dislocations

2009 ◽  
Vol 1224 ◽  
Author(s):  
Sebastián Echeverri Restrepo ◽  
Barend J. Thijsse
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundaries ◽  
Systematic Study ◽  
Degrees Of Freedom ◽  
Minimum Energy ◽  
Local Symmetry ◽  
Virtual Laboratory ◽  
Face Centered Cubic ◽  
Face Centered ◽  
Edge Dislocations

AbstractIn order to perform a systematic study of the interaction between grain boundaries (GBs) and dislocations using molecular dynamics (MD), several tools need to be available. A combination of computational geometry and MD was used to build the foundations of what we call a virtual laboratory. First, an algorithm to generate GBs on face-centered cubic bicrystals was developed. Two crystals with different orientations are placed together. Then, by applying “microscopic” rigid body translations along the GB plane to one of the crystals and removing overlapping atoms, a set of initial configurations is sampled and a minimum energy configuration is found. Second, to classify the geometry of the GBs a local symmetry type (LST) describing the angular environment of each atom is calculated. It is found that for a given relaxed GB the number of atoms with different LSTs is not very large and that it is possible to find unique geometrical patterns in each GB. For instance, the LSTs of two GBs having the same “macroscopic” configuration but different “microscopic” degrees of freedom can be dissimilar: the configurations with higher GB energy tend to have a higher number of atoms with different LSTs. Third, edge dislocations are introduced into the bicrystals. We see that full edge dislocations split into Shockley partials. Finally, by loading the bicrystals with tensile stresses the edge dislocations are put into motion. Various examples of dislocation-GB interactions in Cu are presented.

scholarly journals Micromagnetic Simulation of Thermal Effects in Magnetic Nanostructures

2002 ◽  
Vol 746 ◽  
Author(s):  
Rok Dittrich ◽  
Thomas Schrefl ◽  
Vassilios Tsiantos ◽  
Hermann Forster ◽  
Dieter Suess ◽  
...  
Keyword(s):  
Minimum Energy ◽  
Saddle Points ◽  
Time Integration ◽  
Magnetic Nanostructures ◽  
Integration Scheme ◽  
Thermally Induced ◽  
Thermally Activated ◽  
Time Integration Scheme ◽  
Stochastic Time ◽  
Finding Method

ABSTRACTA path finding method and a stochastic time integration scheme for the simulation of thermally activated magnetization processes are introduced. The minimum energy path and the saddle points for the thermally induced transitions between the ground states of NiFe magnetic nano-elements are calculated.

Computer Simulations of Nonlinear Optical Chromophore Containing Polypeptides

1993 ◽  
Vol 330 ◽  
Author(s):  
Ruth Pachter ◽  
Steven B. Fairchild ◽  
James A. Lupo ◽  
Brian S. Sennett ◽  
Robert L. Crane ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structure Prediction ◽  
Nonlinear Optical ◽  
Integrated Approach ◽  
Genetically Engineered ◽  
Spatial Proximity ◽  
Tertiary Structures ◽  
Eglin C ◽  
Nonlinear Optical Chromophores ◽  
Dynamics Simulations

ABSTRACTIn our continuing efforts towards the design of nonlinear (NLO) optical chromophore containing polypeptides we present an integrated computational approach, in which the design of biomolecular materials with defined secondary and tertiary structures is investigated by means of novel predictive tools, while the effects of the nonlinear optical chromophores are studied with molecular dynamics simulations. A neural network that was trained to predict the spatial proximity of Cα atoms that are less than a given threshold apart, is applied. The double-iterated Kalman filter (DIKF) technique is then employed with a constraints set that includes these pairwise atomic distances, and the distances and angles that define the structure as it is known from the protein's sequence. The results for test cases, particularly Crambin and genetically engineered Eglin-C, demonstrate that this integrated approach is useful for structure prediction at an intermediate resolution. Defined structural motifs of NLO chromophore containing polypeptides are investigated by using molecular dynamics techniques, particularly for the design of coil coiled amphiphatic biopolymers.

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