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Register a new userEfficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
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We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
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It was recently discovered that molecular ionization at high x-ray intensity is enhanced, in comparison with that of isolated atoms, through a phenomenon called CREXIM (charge-rearrangement-enhanced x-ray ionization of molecules). X-ray absorption selectively ionizes heavy atoms within molecules, triggering electron transfer from neighboring atoms to the heavy atom sites and enabling further ionization there. The present theoretical study demonstrates that the CREXIM effect increases with the size of the molecule, as a consequence of increased intramolecular electron transfer from the larger molecular constituents attached to the heavy atoms. We compare x-ray multiphoton ionization dynamics of xenon, iodomethane, and iodobenzene after interacting with an intense x-ray pulse. Although their photoionization cross sections are similar, iodomethane and iodobenzene molecules are more ionized than xenon atoms. Moreover, we predict that the average total charge of iodobenzene is much larger than that of iodomethane, because of the large number of electrons in the benzene ring. The positive charges transferred from the iodine site to the benzene ring are redistributed such that the higher carbon charges are formed at the far end from the iodine site. Our first-principles calculations provide fundamental insights into the interaction of molecules with x-ray free-electron laser (XFEL) pulses. These insights need to be taken into account for interpreting and designing future XFEL experiments.
The advent of x-ray free-electron lasers (XFELs), which provide intense ultrashort x-ray pulses, has brought a new way of creating and analyzing hot and warm dense plasmas in the laboratory. Because of the ultrashort pulse duration, the XFEL-produced plasma will be out of equilibrium at the beginning and even the electronic subsystem may not reach thermal equilibrium while interacting with a femtosecond time-scale pulse. In the dense plasma, the ionization potential depression (IPD) induced by the plasma environment plays a crucial role for understanding and modeling microscopic dynamical processes. However, all theoretical approaches for IPD have been based on local thermal equilibrium (LTE) and it has been controversial to use LTE IPD models for the nonthermal situation. In this work, we propose a non-LTE (NLTE) approach to calculate the IPD effect by combining a quantum-mechanical electronic-structure calculation and a classical molecular dynamics simulation. This hybrid approach enables us to investigate the time evolution of ionization potentials and IPDs during and after the interaction with XFEL pulses, without the limitation of the LTE assumption. In our NLTE approach, the transient IPD values are presented as distributions evolving with time, which cannot be captured by conventional LTE-based models. The time-integrated ionization potential values are in good agreement with benchmark experimental data on solid-density aluminum plasma and other theoretical predictions based on LTE. The present work is promising to provide critical insights into nonequilibrium dynamics of dense plasma formation and thermalization induced by XFEL pulses.
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information that cannot be obtained experimentally. Replica Exchange is an enhanced sampling technique that allows converged results to be obtained faster in comparison to regular molecular dynamics simulations. In this work we report the implementation, also available with GPU-accelerated code, of pH and redox potential (E) as options for multidimensional REMD simulations in AMBER. Previous publications have only reported multidimensional REMD simulations with the temperature and Hamiltonian dimensions. In this work results are shown for N-acetylmicroperoxidase-8 (NAcMP8) axially connected to a histidine peptide. This is a small system that contains only a single heme group. We compare results from E,pH-REMD, E,T-REMD and E,T,pH-REMD to one dimensional REMD simulations and to simulations without REMD. We show that 2D-REMD simulations improve sampling convergence in comparison to 1D-REMD simulations, and that 3D-REMD further improves convergence in comparison to 2D-REMD simulations. Also, our computational benchmarks show that our multidimensional REMD calculations have a small and bearable computational performance, essentially the same as one dimensional REMD. However, in multidimensional REMD a significantly higher number of replicas is required as the number of replicas scales geometrically with the number of dimensions, which requires additional computational resources. In addition to the pH dependence on standard redox potential values and the redox potential dependence on pKa values,we also investigate the influence of the temperature in our results. We observe an agreement between our computational results and theoretical predictions.
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the Constant Chemical Potential Molecular Dynamics (C$mu$MD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$mu$MD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions, and to extract growth rates and free-energy barriers.
The dynamics of a molecule in a magnetic field is significantly different form its zero-field counterpart. One important difference in the presence of a field is the Lorentz force acting on the nuclei, which can be decomposed as the sum of the bare nuclear Lorentz force and a screening force due to the electrons. This screening force is calculated from the Berry curvature and can change the dynamics qualitatively. It is therefore important to include the contributions from the Berry curvature in molecular dynamics simulations in a magnetic field. In this work, we present a scheme for calculating the Berry curvature numerically, by a finite-difference technique, addressing challenges related to the arbitrary global phase of the wave function. The Berry curvature is calculated as a function of bond distance for H$_2$ at the restricted and unrestricted Hartree--Fock levels of theory and for CH$^{+}$ as a function of the magnetic field strength at the restricted Hartree--Fock level of theory. The calculations are carried out using basis sets of contracted Gaussian functions equipped with London phase factors (London orbitals) to ensure gauge-origin invariance. In the paper, we also interpret the Berry curvature in terms of atomic charges and discuss its convergence in basis sets with and without London phase factors. Calculation of the Berry curvature allows for its inclusion in textit{ab initio} molecular dynamics simulations in a magnetic field.
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