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Register a new userSerine Proteases: an Ab Initio Molecular Dynamics Study
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In serine proteases (SPs), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.
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Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, a quantum computer-based AIMD method is presented. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. We compute the energy gradients numerically using the Hellmann-Feynman theorem, finite differences, and a correlated sampling technique. Our method only requires additional classical calculations of electron integrals for each degree of freedom, without any additional computations on a quantum computer beyond the initial VQE run. To achieve comparable accuracy, our gradient calculation method requires three to five orders of magnitude fewer measurements than other brute force methods without correlated sampling. As a proof of concept, AIMD dynamics simulations are demonstrated for the H2 molecule on IBM quantum devices. To the best of our knowledge, it is the first successful attempt to run AIMD on quantum devices for a chemical system. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction (FCI) wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular and material systems.
We extend the ab initio molecular dynamics (AIMD) method based on density functional theory to the nonequilibrium situation where an electronic current is present in the electronic system. The dynamics is treated using the semi-classical generalized Langevin equation. We demonstrate how the full anharmonic description of the inter-atomic forces is important in order to understand the current-induced heating and the energy distribution both in frequency and in real space.
Available simulation methods, suitable to describe solid-solid phase transitions occurring upon increasing of presssure and/or temperature, are based on empirical interatomic potentials: this restriction reduces the predictive power, and thus the general usefulness of numeric simulations in this very relevant field. We present a new simulation scheme which allows, for the first time, the simulation of these phenomena with the correct quantum-mechanical description of interatomic forces and internal stress, along with the correct statistical mechanics of ionic degrees of freedom. The method is obtained by efficiently combining the Car-Parrinello method for ab- initio molecular dynamics with the Parrinello Rahman method to account for a variable cell shape. Within this scheme phase trasformations may spontaneously take place during the simulation with variation of external pressure and/or temperature. The validity of the method is demonstrated by simulating the metal-insulator transition in Silicon (from diamond structure to simple hexagonal structure) under high pressure.
Radium compounds have attracted recently considerable attention due to both development of experimental techniques for high-precision laser spectroscopy of molecules with short-lived nuclei and amenability of certain radium compounds for direct cooling with lasers. Currently, radium monofluoride (RaF) is one of the most studied molecules among the radium compounds, both theoretically and recently also experimentally. Complementary studies of further diatomic radium derivatives are highly desired to assess the influence of chemical substitution on diverse molecular parameters, especially on those connected with laser cooling, such as vibronic transition probabilities, and those related to violations of fundamental symmetries. In this article high-precision emph{ab initio} studies of electronic and vibronic levels of diatomic radium monochloride (RaCl) are presented. Recently developed approaches for treating electronic correlation with Fock-space coupled cluster methods are applied for this purpose. Theoretical results are compared to an early experimental investigation by Lagerqvist and used to partially reassign the experimentally observed transitions and molecular electronic levels of RaCl. Effective constants of $mathcal{P}$-odd hyperfine interaction $W_{rm{a}}$ and $mathcal{P,T}$-odd scalar-pseudoscalar nucleus-electron interaction $W_{rm{s}}$ in the ground electronic state of RaCl are estimated within the framework of a quasirelativistic Zeroth-Order Regular Approximation approach and compared to parameters in RaF and RaOH.
A Molecular Dynamics (MD) study of static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modelled by the classical pair potential proposed by Oeffner and Elliott (OE) [Oeffner R D and Elliott S R 1998, Phys. Rev. B, 58, 14791]. We compare our results to experiments and previous simulations. In addition, an ab initio method, the so-called Car-Parrinello Molecular Dynamics (CPMD), is applied to check the accuracy of the structural properties, as obtained by the classical MD simulations with the OE potential. As in a similar study for SiO2, the structure predicted by CPMD is only slightly softer than that resulting from the classical MD. In contrast to earlier simulations, both the static structure and dynamic properties are in very good agreement with pertinent experimental data. MD simulations with the OE potential are also used to study the relaxation dynamics. As previously found for SiO2, for high temperatures the dynamics of molten GeO2 is compatible with a description in terms of mode coupling theory.
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