STRUCTURAL DYNAMICS OF FREE MOLECULES AND CONDENSED STATE OF MATTER. Part II. TRANSIENT STRUCTURES IN CHEMICAL REACTIONS

Abstract

Basic knowledge of mankind so far relates to the description of electrons and atoms in the material in a state of equilibrium, where the behavior changes slowly over time. The electron diffraction with a high temporal and space resolution has opened the possibility of direct observation of the processes occurring in the transient state of the substance (molecular movie). Here it is necessary to provide a temporary resolution of the order of 100 fs, which corresponds to the transition of the system through the energy barrier of the potential surface, which describes the chemical reaction - the process of the breaking and the formation of new bonds between the interacting agents. Thus, the possibility of the investigation of the coherent nuclear dynamics of molecular systems and the condensed matter can be opened. In the past two decades, it has been possible to observe the nuclear motion in the temporal interval corresponding to the period of the nuclear oscillation. The observed coherent changes in the nuclear system at such temporal intervals determine the fundamental shift from the standard kinetics of chemical reactions to the dynamics of the phase trajectory of a single molecule, the molecular quantum state tomography.

Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone

“…The stability of the conventional hydrogen bonds found in our systems have been monitored by means of semi‐empirical MD simulations until 2 ps. This range of time in the simulation was chosen because bond vibrations and some chemical reactions can be achieved in the range scale between fs and ps 94–96 . Therefore, simulations of 2 ps would be enough to check the stability of our hydrogen bonded systems, which are weaker than covalent bonds involved in chemical reactions.…”

“…We also determined the stability of the conventional hydrogen bonds during the time by performing 2 ps semi‐empirical MD simulations with the PM6‐DH2 Hamiltonian. We chose this time of simulation because bond vibrations and even chemical reactions may be appreciated within this time of simulation and in the case of the conventional hydrogen bonds studied in this work this scale of simulation should be enough to monitories their stability during time 94–96 . The time step of the MD was 1 fs and snapshots were taken from the simulation during each step.…”

Mapping Atomic Motions with Electrons: Toward the Quantum Limit to Imaging Chemistry

“…We define a spatial distribution of orientations of the atomic pairs r ij using a cos 2 ϕ probability function, where ϕ is the angle between the transition dipole and the laser polarization.In CH 3 Br, the transition dipole axis is parallel to r C–Br and defines an angle Ω ij with each atomic pair. Taking a spatial distribution for excitation perpendicular to the electron beam, F ij ( s ) takes the form, where j k ( x ) is the k th order spherical Bessel function. − The change in the structure of CH 3 Br, as the internuclear distance between C–Br increases, is accommodated by referencing the geometrical structure of the molecule. We plot the simulated diffraction intensity sM ( s , t ) for t = 0 and t = T /2, with T being the vibrational period, in Figure c and d, respectively.…”

“…We use the quantum tomographic method to reconstruct the density matrix ρ of the wavepacket. The density matrix elements ρ mn can be expressed in terms of Pr­( r , t ) = |ψ­( r , t )| 2 , by the following formulation, where ­( r , ω m – ω n ) is the Fourier transform of the time dependent probability density Pr­( r , t ) and f mn ( r ) are the pattern functions. , where Ψ m ( r ) and ϕ n ( r ) are the normalized regular and non-normalizable irregular wave function of the Schrödinger equation. − The calculated pattern functions f mn ( r ) for the first three vibrational levels are depicted in Figure a. Gaussian quadrature for the integration is used for the integration.…”