Evaluating Variational Quantum Eigensolver Approaches for Simplified Models of Molecular Systems: A Case Study on Protocatechuic Acid.

The Variational Quantum Eigensolver (VQE) is a hybrid algorithm that combines quantum and classical computing to determine the ground-state energy of molecular systems. In this context, this study applies VQE to investigate the ground state of protocatechuic acid, analyzing its performance with various Ansatzes and active spaces. Subsequently, all VQE results were compared to those obtained with the CISD and FCI methods.

An artificial neural network model to predict structure-based protein-protein free energy of binding from Rosetta-calculated properties.

The prediction of the free energy (Δ) of binding for protein-protein complexes is of general scientific interest as it has a variety of applications in the fields of molecular and chemical biology, materials science, and biotechnology. Despite its centrality in understanding protein association phenomena and protein engineering, the Δ of binding is a daunting quantity to obtain theoretically. In this work, we devise a novel Artificial Neural Network (ANN) model to predict the Δ of binding for a given three-dimensional structure of a protein-protein complex with Rosetta-calculated properties.

Electron nuclear dynamics with plane wave basis sets: complete theory and formalism.

Electron nuclear dynamics (END) is an ab initio quantum dynamics method that adopts a time-dependent, variational, direct, and non-adiabatic approach. The simplest-level (SL) END (SLEND) version employs a classical mechanics description for nuclei and a Thouless single-determinantal wave function for electrons. A higher-level END version, END/Kohn-Sham density functional theory, improves the electron correlation description of SLEND.

Symmetry-breaking effects on time-dependent dynamics: correct differential cross sections and other properties in H + CH at E = 30 eV.

We present a computational procedure that introduces low degrees of symmetry breaking into a restricted Hartree-Fock (RHF) state in order to induce higher symmetry breaking during the state's subsequent dynamics. The symmetries herein considered are those of electronic HF states as classified by Fukutome; those symmetries affect bond dissociations and internal rotations among other phenomena. Therefore, this investigation extends a part of Fukutome's time-independent analysis of symmetry breaking to the time-dependent (dynamical) regime.

Electron Nuclear Dynamics Simulations of Proton Cancer Therapy Reactions: Water Radiolysis and Proton- and Electron-Induced DNA Damage in Computational Prototypes.

Proton cancer therapy (PCT) utilizes high-energy proton projectiles to obliterate cancerous tumors with low damage to healthy tissues and without the side effects of X-ray therapy. The healing action of the protons results from their damage on cancerous cell DNA. Despite established clinical use, the chemical mechanisms of PCT reactions at the molecular level remain elusive.

Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6.

To elucidate microscopic details of proton cancer therapy (PCT), we apply the simplest-level electron nuclear dynamics (SLEND) method to H+ + (H2O)1-6 at ELab = 100 keV. These systems are computationally tractable prototypes to simulate water radiolysis reactions-i.e.

Understanding the Reactivity and Regioselectivity of Methylation of Nitronates [R(1)R(2)CNO2](-) by CH3I in the Gas Phase.

Methylation of [R(1)R(2)CNO2](-), where R(1) = R(2) = H (1), R(1) = CH3 and R(2) = H (2), R(1) = R(2) = CH3 (3), and R(1) + R(2) = c-(CH2)2 (4), by CH3I was studied by an ab initio MP2/CBS method, RRKM theory, and kinetic simulations. Contrary to a previous proposal for the reaction mechanism, C-methylation is the preferred pathway of thermodynamics and kinetics. This is corroborated by the agreement between the calculated and experimental reactivity trend 4 ≫ 3 > 2 > 1.