Quantum Mechanical Dynamics Research Articles

Molecular Dynamics of the Davies Ambimodal C-H Functionalization/Cope Rearrangement Reaction.

The mechanism of the dirhodium-catalyzed combined C-H functionalization/Cope rearrangement (CH/Cope) reaction discovered by the Davies group has been investigated with density functional theory (DFT) calculations and quasi-classical molecular dynamics (MD) simulations. Computations from the Davies group previously showed that there is a post-transition state bifurcation leading to a direct CH reaction and also to the CH/Cope product. While this work was in preparation, the Tantillo group and the Ess group independently reported quantum mechanical and molecular dynamics studies on the dirhodium-tetracarboxylate-catalyzed diazoester CH/Cope and CH insertion reactions with 1,3-cyclohexadiene and 1,4-cyclohexadiene, respectively. The Tantillo group cited "dynamic mismatching" to explain the origins of the low yield of CH/Cope products in some experiments; the Ess group explained the origins of product selectivity from the perspective of TS vibrational modes and their synchronization that occurs at the entropic intermediates. We report quasi-classical trajectories for the reaction of the carbene with 1-methylcyclohexene that afford both the CH/Cope and C-H insertion products. After passing through the transition state that involves mostly hydrogen transfer, momentum drives the reaction trajectories toward the CH/Cope products.

The effect of hypo‐sulfonamide accelerators on the induction period of rubber vulcanization based on experiments and molecular simulations

AbstractAccelerators are indispensable additives in rubber vulcanization reactions. Hypo‐sulfonamide accelerators are widely used due to their fast vulcanization speed. However, the short vulcanization induction period compromises the processing safety of rubber. In this paper, we incorporated experiments with molecular simulations to investigate the underlying reasons for the different effects of various hypo‐sulfonamide accelerators The vulcanization induction period of each accelerator was investigated according to the vulcanization curves. Furthermore, the corresponding reaction mechanism was explored from the molecular scale through quantum mechanical and molecular dynamics simulations. Subsequently, the research focus was discussed in depth. The compatibility relationship between the accelerators and the rubber materials was verified through the crosslinking density test, and a coincidence between the experimental and simulation results was found. This study guides the selection and improvement of hypo‐sulfonamide accelerators and corroborates the factors influencing the vulcanization induction period of natural rubber by accelerators.Highlights Reactivity of accelerators calculated by quantum mechanical simulations. Difference in solubility parameter characterizes accelerator/NR compatibility. Mobility and diffusion coefficient reflect the diffusion ability of the promoter. Molecular simulation results are consistent with experimental results.

A model of ionization-induced reactions in CH4/N2 clusters in Titan's atmosphere: theoretical insights into mono- and divalent states

Abstract We propose a model for ionization-induced reactions between N2 and CH4, the main components of Titan's atmosphere, and examine their mechanism using quantum mechanical and molecular dynamics methods. Bimolecular CH4–N2 clusters form through collision, and their conformation depends on the encounter cross section due to weak intermolecular interaction. These clusters acquire a driving force through vertical ionization because the vertically ionized structure is not situated at the minimum of the potential energy surface in the ionized state. This leads to multiple reactions, overcoming energy barriers in the process. In the divalent state, a robust attractive interaction occurs between CH4 and N2 through charge transfer. Subsequently, the H4C–N2 covalent bond forms prior to reactions, resulting in the production of N2H+, CH3+, CH3N2+, and CH2N2+; otherwise only N2H+, CH3+, and CH2+ are generated. In contrast, when ionized to a monovalent state, although dissociation of N2H+ and isomerization to CH3NHN+ and CH3NNH+ occurs, a significant portion dissociates into CH4+ and N2 without undergoing further reactions. Additionally, the generation of N2H+ and CH3+ is limited in the monovalent state, primarily due to a lower driving force and the absence of Coulombic explosion. Our computational results highlight the pivotal role of divalent reactions within Titan's atmosphere, which are more efficient than monovalent reactions.

Quantum-mechanical four-body versus semi-classical three-body theories for double charge exchange in collisions of fast alpha particles with helium targets

AbstractWithin the two-channel distorted wave second-order perturbative theoretical formalism, we study capture of both electrons from helium-like targets by heavy nuclei as projectiles at intermediate and high impact energies. The emphasis is on the four-body single-double scattering (SDS-4B) method and the three-body continuum distorted wave impact parameter method (CDW-3B-IPM). The SDS-4B method deals with the full quantum-mechanical correlative dynamics of all the four interactively participating particles (two electrons, two nuclei). The CDW-3B-IPM is a semi-classical three-body independent particle model (one electron, two nuclei), using a combinatorial calculus to describe double capture by a product of two uncorrelated probabilities, integrated over impact parameters. Both theories share a common feature in having altogether two electronic full Coulomb continuum wave functions. One such function is centered on the projectile nucleus in the entrance channel, whereas the other is centered on the target nucleus in the exit channel. These two methods satisfy the correct initial and final Coulomb boundary conditions in the asymptotic region of scattering, at infinitely large inter-particle separations. Yet, it is presently demonstrated that most of the available experimental data on total cross sections for the double capture from helium by alpha particles distinctly favor the SDS-4B method. This is especially true at intermediate energies. Such energies are critically important in versatile applications under the general umbrella of ion transport in matter, including thermonuclear fusion (plasma physics) and ion therapy (medicine).

Longitudinal relaxation and quantum spin dynamics in Dzyaloshinsky–Moriya interaction spin spiral dimers

The spin dynamics of a quantum mechanical spin dimer with exchange and Dzyaloshinsky–Moriya interaction are investigated. The spin dimer shows a periodic longitudinal relaxation between the initial and inverted spin spiral state. The calculations were accomplished analytically using a coordinate transfer to local coordinates. Additionally, the dimer is investigated numerically by solving the Gisin–Schrödinger equation. The influence of damping and an external magnetic field perpendicular to the spiral plane has been considered. The spin dynamics were categorized into classical and quantum mechanical spin dynamics. In order to distinguish between classical and quantum spin states, the von Neumann entropy was calculated, which characterizes the entanglement change during the longitudinal reversal.

Computational Assessment of a Dual-Action Ru(II)-Based Complex: Photosensitizer in Photodynamic Therapy and Intercalating Agent for Inducing DNA Damage.

A combined quantum-mechanical and classical molecular dynamics study of a recent Ru(II) complex with potential dual anticancer action is reported here. The main basis for the multiple action relies on the merocyanine ligand, whose electronic structure allows the drug to be able to absorb within the therapeutic window and in turn efficiently generate 1O2 for photodynamic therapy application and to intercalate within two nucleobases couples establishing reversible electrostatic interactions with DNA. TDDFT outcomes, which include the absorption spectrum, triplet states energy, and spin-orbit matrix elements, evidence that the photosensitizing activity is ensured by an MLCT state at around 660 nm, involving the merocyanine-based ligand, and by an efficient ISC from such state to triplet states with different characters. On the other hand, the MD exploration of all the possible intercalation sites within the dodecamer B-DNA evidences the ability of the complex to establish several electrostatic interactions with the nucleobases, thus potentially inducing DNA damage, though the simulation of the absorption spectra for models extracted by each MD trajectory shows that the photosensitizing properties of the complex remain unaltered. The computational results support that the anti-tumor effect may be related to multiple mechanisms of action.

Dynamic Effects on the Ionization-Induced Reactions of Methyl Halides: Quantum Mechanical and Molecular Dynamics Studies.

The mechanisms of the ionization-induced fragmentation and H migration of methyl halides CH3X (X = F, Cl, Br) have been examined by quantum mechanical and molecular dynamics methods. When CH3X (X = F, Cl, Br) is vertically ionized into a divalent cation, it can obtain enough excess energy to overcome the energy barrier of subsequent reaction channels for the formation of H+, H2+, and H3+ species and intramolecular H migration. The product distributions of these species greatly depend on the halogen atoms. The H+ formation decreases in the order of F > Cl > Br, which is inversely proportional to the increase in the magnitude of the energy barrier in the order of Br > Cl > F. This is attributable to the change in the charge distribution of the entire molecule by the halogen atoms. Meanwhile, the small H migration ratio for Cl and Br, despite their low energy barriers, was explained by the small sum of states at the transition state based on the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The H3+ formation ratio is unexpectedly smaller despite its low energy barrier. This is attributed to the dynamic effects of the H2 roaming that always occur prior to the reaction in question. Molecular dynamics simulations showed that the H2 roaming was restricted in a certain area due to an initially produced driving force on the hydrogen atoms in a certain direction by vertical ionization; this phenomenon suppresses the formation of H3+, which requires the hydrogen atoms to be in motion over a relatively wide range to enter the transition state region. Thus, the low proportion of the observed H3+ can be explained by the dynamical probability of the transition state structure formation.

Asphaltene aggregation under the influence of structural features and interaction energies: Combination of quantum mechanical and molecular dynamics approaches

The importance of the model to predict the aggregation behavior of asphaltene molecules at the molecular level was well established in different studies. Elucidation of the relationship between the interaction energy and the structural characteristics of asphaltene molecules to their aggregation behavior still needs further investigation. For this purpose, we combined the quantum mechanics and molecular dynamics approaches and analyzed the interaction energy of asphaltene to find out the effect of structural features on the aggregation behavior. The interaction energy of asphaltene is used in this study to evaluate the potential of aggregation. We found that asphaltene molecules with smaller aromatic cores and shorter side chains form longer but more unstable stacks in the aggregation phase. If these structures do not have polar groups in the side chains, they will not show significant aggregation behavior in the clustering phase. Also, the length of stacks formed in the accumulation phase can be interpreted and predicted based on the terms such as attractive dispersion energy and steric repulsion in the interaction energy of asphaltene dimers. The aggregation process is explained by analyzing the nature of the interaction energy. As a result, by examining the effect of structural features on interaction energy, a relatively acceptable picture of the aggregation behavior of the asphaltene molecules can be obtained.

An in silico study of sustainable drug pollutants removal using carboxylic acid functionalized-MOF nanostructures (MIL-53 (Al)-(COOH)2): Towards a greener future

Emerging environmental pollutants have become a major environmental challenge due to the highly toxic effluents produced by industries. Among these emerging pollutants, pharmaceutical drugs, which are consumed and are highly soluble, lead to the severe degradation of water resources. To address this issue, adsorptive capturing methods have been considered as a potential solution due to their efficiency and environmental compatibility. This study focuses on the use of carboxylic acid functionalized MIL-53 (Al) (CA/MIL-53 (Al)) for the removal of pharmaceutical pollutants (PhPs) such as acetaminophen, ibuprofen, aspirin and methyl salicylate. The study was conducted employing quantum mechanical (QM), Monte Carlo (MC) and molecular dynamics (MD) simulations. The results of QM analysis exhibited that the functionalization of MIL-53 (Al) with carboxylic acid (CA) groups improved its adsorption affinity. Moreover, the MOF-water-Ibuprofen mixed configurations showed higher chemical reactivity and adsorption capacity. It was demonstrated that the MIL-53 (Al) adsorption characteristics were significantly improved following its functionalization with CA groups. This study highlights the potential of functionalized MOFs as a promising solution for PhPs removal from water resources. The results of this study provide valuable information for further research and the development of new adsorbents for the removal of emerging pollutants in the environment.

Statistical properties of the two dimensional Feshbach–Villars oscillator (FVO) in the rotating cosmic string space–time

This paper focuses on the quantum mechanical dynamics of a massive and spinless relativistic particle in space–time generated by a rotating cosmic string. The equations of motion are found by the use of the Feshbach–Villars formulation of the Klein–Gordon equation. The wave functions and related energies have been deduced. Subsequently, the partition function was approached with the help of the representation of the Zeta function. Through this function, thermal properties are reported. The behavior of these properties in relation to the physical parameters of the model such as rotation, curvature and quantum numbers was investigated. Moreover, the impact of the topological defect on the quantum system under investigation is discussed.

Multiscale Modeling of Ion Dynamics in Memristive Elements

A multiscale computational scheme is proposed for ion dynamics that allows modeling based on primary information—data on the chemical composition of the material and its crystal structure. The scheme includes quantum mechanical and molecular dynamics modeling as well as Monte Carlo simulation of ion and electron dynamics taking into account the real crystal structure. Approbation of the proposed approach is carried out on a silicon oxide memristive element. The results of computational experiments are presented that demonstrate the stages of growth and destruction of a conductive filament under the action of a time-varying voltage.

Mechanism of the Stereoselective Catalysis of Diels-Alderase PyrE3 Involved in Pyrroindomycin Biosynthesis.

The biosynthesis of pyrroindomycins A and B features a complexity-building [4 + 2] cycloaddition cascade, which generates the spirotetramate core under the catalytic effects of monofunctional Diels-Alderases PyrE3 and PyrI4. We recently showed that the main functions of PyrI4 include acid catalysis and induced-fit/conformational selection. We now present quantum mechanical and molecular dynamics studies implicating a different mode of action by PyrE3, which prearranges an anionic polyene substrate into a high-energy reactive conformation at which an inverse-electron-demand Diels-Alder reaction can occur with a low barrier. Stereoselection is realized by strong binding interactions at the endo stereochemical relationship and a local steric constraint on the endo-1,3-diene unit. These findings, illustrating distinct mechanisms for PyrE3 and PyrI4, highlight how nature has evolved multiple ways to catalyze Diels-Alder reactions.

Matrix-Model Simulations Using Quantum Computing, Deep Learning, and Lattice Monte Carlo

Matrix quantum mechanics plays various important roles in theoretical physics, such as a holographic description of quantum black holes, and it underpins the only practical numerical approach to the study of complex high-dimensional supergravity theories. Understanding quantum black holes and the role of entanglement in a holographic setup is of paramount importance for the realization of a quantum theory of gravity. Moreover, a complete numerical understanding of the holographic duality and the emergence of geometric space-time features from microscopic degrees of freedom could pave the way for new discoveries in quantum information science. Euclidean lattice Monte Carlo simulations are the de facto numerical tool for understanding the spectrum of large matrix models and have been used to test the holographic duality. However, they are not tailored to extract dynamical properties or even the quantum wave function of the ground state of matrix models. Quantum computing and deep learning provide potentially useful approaches to study the dynamics of matrix quantum mechanics. If successful in the context of matrix models, these rapidly improving numerical techniques could become the new Swiss army knife of quantum gravity practitioners. In this paper, we perform the first systematic survey for quantum computing and deep-learning approaches to matrix quantum mechanics, comparing them to lattice Monte Carlo simulations. These provide baseline benchmarks before addressing more complicated problems. In particular, we test the performance of each method by calculating the low-energy spectrum.22 MoreReceived 23 August 2021Accepted 20 December 2021DOI:https://doi.org/10.1103/PRXQuantum.3.010324Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.Published by the American Physical SocietyPhysics Subject Headings (PhySH)Research AreasLattice gauge theoryMachine learningQuantum algorithmsSupersymmetric field theoriesTechniquesHybrid Monte Carlo algorithmPath-integral Monte CarloQuantum InformationParticles & Fields

Quantum mechanical and molecular dynamics simulations of retinal systems utilizing novel artificial-intelligence-derived force fields

G-protein-coupled receptors (GPCRs) are a superfamily of transmembrane proteins that perform diverse signaling roles in organisms, including humans. This makes them an attractive target for pharmaceuticals, with 134 different GPCRs being currently targeted by roughly 700 drugs. Here we studied the retinylidene cofactor of GPCR rhodopsin that is responsible for initiating phototransduction in many organisms. The conformational energy landscape of this retinylidene is both complex and critical for the activation of the rhodopsin protein, which depends not only on specific isomers but on rotamers as well.

Absorption behavior of doxorubicin hydrochloride in visible region in different environments: a combined experimental and computational study.

The experimental absorption measurements in the interval 350-600 nm (Vis), molecular dynamics simulations, quantum-mechanics calculations and an advanced molecular treatment of simulation data are here combined to provide a complete picture of the absorption behavior in the visible portion of the electromagnetic spectrum of the doxorubicin hydrochloride (DX) molecule in different environments. By such an approach, we have shown that it is possible to characterize the effect of the environment on the DX absorption behavior - including the vibronic contributions - as well as to interpret such differences in terms of molecular electronic excited states, which are found to be strongly influenced by the environment.

Early steps of oxidative damage in DNA quadruplexes are position-dependent: quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized Guanine.

Early steps of oxidative damage in DNA quadruplexes are position-dependent: quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized Guanine.

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

Guanine radical cation (G•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)3 (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G•+ (Tel21+). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21+ systems, differing in the position of G•+ in the sequence. When G•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na+ ions and increase the solvent exposed surface of G•+. Analysis of solvation patterns of G•+ provides new insights on the main reactions of G•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.

Theoretical Simulations of Thermochromic and Aggregation-Induced Emission Behaviors of a Series of Red-Light Anthracene-o-carborane Derivatives.

Quantum mechanical and molecular dynamics simulations have been carried out on a series of anthracene-o-carborane derivatives (ANT-H, ANT-Ph, ANT-Me and ANT-TMS) with rare red-light emission in the solid state. The simulation of the heating process of the crystals and further comparison of the molecular structures and excited-state properties before and after heating help us to disclose the thermochromic behavior, that is, the red-shift emission is caused by elongation of the C1-C2 bond in the carborane moiety after heating. Thus, we believe that the molecular structure in the crystal is severely affected by heating. Transformation of the molecular conformation appears in the ANT-H crystal with increasing temperature. More specifically, the anthracene moiety moves from nearly parallel to the C1-C2 bond to nearly perpendicular, causing the short-wavelength emission to disappear after heating. As for the aggregation-induced emission phenomenon, the structures and photophysical properties were investigated comparatively in both the isolated and crystal states; the results suggested that the energy dissipation in crystal surroundings was greatly reduced through hindering structure relaxation from the excited to the ground state. We expect that discussion of the thermochromic behavior will provide a new analysis perspective for the molecular design of o-carborane derivatives.

On the quantum and classical control of laser-driven isomerization in the Wigner representation.

We investigate the validity of the classical approximation to the numerically exact quantum dynamics for infrared laser-driven control of isomerization processes. To this end, we simulate the fully quantum mechanical dynamics both by wavepacket propagation in position space and by propagating the Wigner function in phase space employing a quantum-mechanical correction term. A systematic comparison is made with purely classical propagation of the Wigner function. On the example of a one-dimensional double well potential, we identify two complementary classes of pulse sequences that invoke either a quantum mechanically or a classically dominated control mechanism. The quantum control relies on a sequence of excitations and de-excitations between the system's eigenstates on a time scale far exceeding the characteristic vibrational oscillation periods. In contrast, the classical control mechanism is based on a short and strong few-cycle field exerting classical-like forces driving the wavepacket to the target potential well where it is slowed down and finally trapped. While in the first case, only the quantum mechanical propagation correctly describes the field-induced population transfer, the short pulse case is also amenable to a purely classical description. These findings shed light on the applicability of classical approximations to simulate laser-controlled dynamics and may offer a guideline for novel control experiments in more complex systems that can be analyzed and interpreted utilizing efficient state-of-the-art classical trajectory simulations based on ab initio molecular dynamics.

General theory of non-reversible local dynamics

A general theory of dynamics is formulated with the aim of its application in emergent quantum mechanics. In such a framework, it is argued that the fundamental dynamics of emergent quantum mechanics must be non-reversible.