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We present a practical semiclassical method for computing the electron spin dynamics of a radical in which the electron spin is hyperfine coupled to a large number of nuclear spins. This can be used to calculate the singlet and triplet survival probabilities and quantum yields of radical recombination reactions in the presence of magnetic fields. Our method differs from the early semiclassical theory of Schulten and Wolynes [J. Chem. Phys. 68, 3292 (1978)] in allowing each individual nuclear spin to precess around the electron spin, rather than assuming that the hyperfine coupling-weighted sum of nuclear spin vectors is fixed in space. The downside of removing this assumption is that one can no longer obtain a simple closed-form expression for the electron spin correlation tensor: our method requires a numerical calculation. However, the computational effort increases only linearly with the number of nuclear spins, rather than exponentially as in an exact quantum mechanical calculation. The method is therefore applicable to arbitrarily large radicals. Moreover, it approaches quantitative agreement with quantum mechanics as the number of nuclear spins increases and the environment of the electron spin becomes more complex, owing to the rapid quantum decoherence in complex systems. Unlike the Schulten-Wolynes theory, the present semiclassical theory predicts the correct long-time behaviour of the electron spin correlation tensor, and it therefore correctly captures the low magnetic field effect in the singlet yield of a radical recombination reaction with a slow recombination rate. [ABSTRACT FROM AUTHOR]

A statistical model based on the quasiclassical trajectory method is presented in this work for atom-diatom insertion reactions. The basic difference between this and the corresponding statistical quantum model (SQM) lies in the fact that trajectories instead of wave functions are propagated in the entrance and exit channels. Other than this the two formulations are entirely similar. In particular, it is shown that conservation of parity can be taken into account in a natural and precise way in the statistical quasiclassical trajectory (SQCT) model. Additionally, the SQCT model complies with the principle of detailed balance and overcomes the problem of the zero point energy in the products. As a test, the model is applied to the H3+ and H+D2 exchange reactions. The excellent agreement between the SQCT and SQM results, especially in the case of the differential cross sections, indicates that the effect of tunneling through the centrifugal barrier is negligible. The effect of ignoring quantum mechanical parity conservation is also investigated. [ABSTRACT FROM AUTHOR]

A new method for solving the close coupled equations of inelastic scattering is presented. The method is based on Johnson’s log derivative algorithm, and uses the same quadrature for the solution of the corresponding integral equations. However it differs from the original method in the use of a piecewise constant diagonal reference potential. This results in a reduction in matrix operations at subsequent energies, and an improved convergence of the solution with respect to the number of grid points. These advantages are clearly demonstrated when our method is applied to an atom–diatom rotational excitation problem. [ABSTRACT FROM AUTHOR]

The water molecule, rotationally state selected in the third and fourth OH stretching overtone (|04>-, |05>-) and stretch–bend combination (|04-2>) levels, has been photodissociated via the A state at λ[bar_over_tilde:_approx._equal_to]282 nm. The photofragment rotational state distributions, determined by OH(A–X) laser induced fluorescence (LIF), differ from those reported previously by Andresen and co-workers, in which water was initially prepared in the |01>- level and photodissociated at 193 nm, and from those by Crim and co-workers, in which H2O was photodissociated via the |04>- level at wavelengths shorter than 282 nm. These differences become more pronounced with increasing angular momentum in the parent water molecule and with an increasing number of quanta in the intermediate OH stretching overtone state. The Franck–Condon theory of Balint-Kurti, previously employed successfully to account for the product state distributions arising from the 193 nm photodissociation of H2O|01>-, qualitatively reproduces the trends observed in the present study if it is assumed that dissociation occurs preferentially from extended RH-OH configurations of the |04>- and |05>- overtones. The product OH state distributions are thus shown to be sensitive indicators of the bending and rotational motions of H2O(X) in the wide amplitude stretching region of the ground state surface. [ABSTRACT FROM AUTHOR]

The intricate hydrogen-bonded network of water gives rise to various structures with anomalous properties at different thermodynamic conditions. Nanoconfinement can further modify the water structure and properties, and induce specific water motifs, which are instrumental for technological applications such as atmospheric water harvesting. However, so far, a causal relationship between nanoconfinement and the presence of specific hydrophilic adsorption sites is lacking, hampering the further design of nanostructured materials for water templating. Therefore, this work investigates the organisation of water in zirconium-based metal-organic frameworks (MOFs) with varying topologies, pore sizes, and chemical composition, to extract design rules to shape water. The highly tuneable pores and hydrophilicity of MOFs makes them ideally suited for this purpose. We find that small nanopores favour orderly water clusters that nucleate at hydrophilic adsorption sites. Favourably positioning the secondary adsorption sites, hydrogen-bonded to the primary adsorption sites, allows larger clusters to form at moderate adsorption conditions. To disentangle the importance of nanoconfinement and hydrophilic nucleation sites in this process, we introduce an analytical model with precise control of the adsorption sites. This sheds a new light on design parameters to induce specific water clusters and hydrogen-bonded networks, thus rationalising the application space of water in nanoconfinement., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

The transport of excess protons in water is central to acid-base chemistry, biochemistry and energy production. However, elucidating its mechanism has been challenging. Recent nonlinear vibrational spectroscopy experiments could not be explained by existing models. Here we use both vibrational spectroscopy calculations and neural-network-based molecular dynamics simulations that account for nuclear quantum effects for all atoms to determine the proton transport mechanism. Our simulations reveal an equilibrium between two stable proton-localized structures with distinct Eigen-like and Zundel-like hydrogen-bond motifs. Proton transport follows a three-step mechanism gated by two successive hydrogen-bond exchanges: the first reduces the proton-acceptor water coordination, leading to proton transfer, and the second, the rate-limiting step, prevents rapid back-transfer by increasing the proton-donor coordination. This sequential mechanism is consistent with experimental characterizations of proton diffusion, explaining the low activation energy and the prolonged intermediate lifetimes in vibrational spectroscopy. These results are crucial for understanding proton dynamics in biochemical and technological systems., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Vibrational spectroscopy allows us to understand complex physical and chemical interactions of molecular crystals and liquids such as ammonia, which has recently emerged as a strong hydrogen fuel candidate to support a sustainable society. We report inelastic neutron scattering measurement of vibrational properties of ammonia along the solid-to-liquid phase transition with high enough resolution for direct comparisons to ab-initio simulations. Theoretical analysis reveals the essential role of nuclear quantum effects (NQEs) for correctly describing the intermolecular spectrum as well as high energy intramolecular N-H stretching modes. This is achieved by training neural network models using ab-initio path-integral molecular dynamics (PIMD) simulations, thereby encompassing large spatiotemporal trajectories required to resolve low energy dynamics while retaining NQEs. Our results not only establish the role of NQEs in ammonia but also provide general computational frameworks to study complex molecular systems with NQEs., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond the reach of current classical-digital simulation. To identify a 'quantum advantage' for these simulations, performance analysis of both analog-quantum simulation on noisy hardware and classical-digital algorithms is needed. In this Review, we make a comparison between a noisy analog trapped-ion simulator and a few choice classical-digital methods on simulating the dynamics of a model molecular Hamiltonian with linear vibronic coupling. We describe several simple Hamiltonians that are commonly used to model molecular systems, which can be simulated with existing or emerging trapped-ion hardware. These Hamiltonians may serve as stepping stones towards the use of trapped-ion simulators for systems beyond the reach of classical-digital methods. Finally, we identify dynamical regimes in which classical-digital simulations seem to have the weakest performance with respect to analog-quantum simulations. These regimes may provide the lowest hanging fruit to make the most of potential quantum advantages., (© 2024. Springer Nature Limited.)

Hybrid atom-ion systems are a rich and powerful platform for studying chemical reactions, as they feature both excellent control over the electronic state preparation and readout as well as a versatile tunability over the scattering energy, ranging from the few-partial wave regime to the quantum regime. In this work, we make use of these excellent control knobs, and present a joint experimental and theoretical study of the collisions of a single 138Ba+ ion prepared in the 5 d 2 D 3 / 2 , 5 / 2 metastable states with a ground state 6Li gas near quantum degeneracy. We show that in contrast to previously reported atom-ion mixtures, several non-radiative processes, including charge exchange, excitation exchange and quenching, compete with each other due to the inherent complexity of the ion-atom molecular structure. We present a full quantum model based on high-level electronic structure calculations involving spin-orbit couplings. Results are in excellent agreement with observations, highlighting the strong coupling between the internal angular momenta and the mechanical rotation of the colliding pair, which is relevant in any other hybrid system composed of an alkali-metal atom and an alkaline-earth ion. [ABSTRACT FROM AUTHOR]

Close-coupling scattering calculations have been carried out to predict the magnitude of electric fields required to dissociate specific vibration-rotation levels in H2+. Results for electric fields up to 40 kV cm-1, which may dissociate levels up to 25 cm-1 below the dissociation limit, are presented. The results are used to simulate spectra which are compared with experimental spectra. A method for extracting the eigenphase sum from a coupled channel scattering calculation is described in the appendix and used in the calculations. [ABSTRACT FROM AUTHOR]

Mechanisms occurring at the atomic level are now known to drive processes essential for life, as revealed by quantum effects on biochemical reactions. Some macroscopic characteristics of organisms may thus show an atomic imprint, which may be transferred across organisms and affect their evolution. This possibility is considered here for the first time, with the aim of elucidating the appearance of an animal innovation with an unclear evolutionary origin: migratory behaviour. This trait may be mediated by a radical pair (RP) mechanism in the retinal flavoprotein cryptochrome, providing essential magnetic orientation for migration. Isotopes may affect the performance of quantum processes through their nuclear spin. Here, we consider a simple model and then apply the standard open quantum system approach to the spin dynamics of cryptochrome RP. We changed the spin quantum number (I) and g-factor of hydrogen and nitrogen isotopes to investigate their effect on RP's yield and magnetic sensitivity. Strong differences arose between isotopes with I = 1 and I = 1/2 in their contribution to cryptochrome magnetic sensitivity, particularly regarding Earth's magnetic field strengths (25-65 µT). In most cases, isotopic substitution improved RP's magnetic sensitivity. Migratory behaviour may thus have been favoured in animals with certain isotopic compositions of cryptochrome., (© 2023 The Authors. BioEssays published by Wiley Periodicals LLC.)

Quantum biology is a modern field of research that aims to understand how quantum effects can affect the chemistry underlying various biological processes. This paper reviews several examples of biological processes where quantum effects might play a notable role. Initially, the photon capture mechanism present in vision is discussed, where the energy of the photon is used to cause conformational changes to chromophoric proteins. The second example elaborates the highly efficient energy transfer process present in photosynthesis and discusses, in particular, how the random quantum walk process may enhance the performance drastically. Subsequently, the vertebrate magnetoreception, and the possible associated role of the radical pair mechanism in the process is considered. The review concludes with the discussion of some speculative ideas of putative quantum effects arising in neural processes. [ABSTRACT FROM AUTHOR]

The dissociation of methane is not only an important reaction step in catalytic processes, but also of fundamental interest. Dynamical effects during the dissociative chemisorption of methane on metal surfaces cause significant differences in computed reaction rates, compared to what is predicted by typical transition state theory (TST) models. It is clear that for a good understanding of the catalytic activation of methane dynamical simulations are required. In this paper, a general blueprint is provided for performing dynamical simulations of the dissociative chemisorption of methane on metal surfaces, by employing either the quasi-classical trajectory or ring polymer molecular dynamics approach. If the computational setup is constructed with great care-since results can be affected considerably by the setup - chemically accurate predictions are achievable. Although this paper concerns methane dissociation, the provided blueprint is, so far, applicable to the dissociative chemisorption of most molecules. [ABSTRACT FROM AUTHOR]

Fullerenes, as characteristic carbon nanomaterials, offer significant potential for diverse applications due to their structural diversity and tunable properties. Numerous isomers can exist for a specific fullerene size, yet a comprehensive understanding of their fundamental properties remains elusive. In this study, we construct an up-to-date computational database for C20–C60 fullerenes, consisting of 5770 structures, and calculate 12 fundamental properties using DFT, including stability (binding energy), electronic properties (HOMO-LUMO gap), and solubility (partition coefficient logP). Our findings reveal that the HOMO-LUMO gap weakly correlates with both binding energy and logP, indicating that electronic properties can be tailored for specific uses without affecting stability or solubility. In addition, we introduce a set of topological features and geometric measures to investigate structure-property relationships. We apply atom, bond, and hexagon features to effectively predict the stability of C20–C60 fullerenes, surpassing the conventional qualitative isolated pentagon rule, and demonstrating their robust transferability to larger-size fullerenes beyond C60. Our work offers guidance for optimizing fullerenes as electron acceptors in organic solar cells and lays a foundational understanding of their functionalization and applications in energy conversion and nanomaterial sciences. [ABSTRACT FROM AUTHOR]

Cryptochromes (CRYs), which are signaling proteins related to DNA photolyases, play pivotal roles in sensory responses throughout biology, including growth and development, metabolic regulation, circadian rhythm entrainment and geomagnetic field sensing. This review explores the evolutionary relationships and functional diversity of cryptochromes from the perspective of their molecular structures. In general, CRY biological activities derive from their core structural architecture, which is based on a Photolyase Homology Region (PHR) and a more variable and functionally specific Cryptochrome C-terminal Extension (CCE). The α/β and a-helical domains within the PHR bind FAD, modulate redox reactive residues, accommodate antenna cofactors, recognize small molecules and provide conformationally responsive interaction surfaces for a range of partners. CCEs add structural complexity and divergence, and in doing so, influence photoreceptor reactivity and tailor function. Primary and secondary pockets within the PHR bind myriad moieties and collaborate with the CCEs to tune recognition properties and propagate chemical changes to downstream partners. For some CRYs, changes in homo and hetero-oligomerization couple to light-induced conformational changes, for others, changes in posttranslational modifications couple to cascades of protein interactions with partners and effectors. The structural exploration of cryptochromes underscores how a broad family of signaling proteins with close relationship to light-dependent enzymes achieves a wide range of activities through conservation of key structural and chemical properties upon which function-specific features are elaborated. [ABSTRACT FROM AUTHOR]

Machine learning interatomic potentials are revolutionizing large-scale, accurate atomistic modeling in material science and chemistry. Many potentials use atomic cluster expansion or equivariant message-passing frameworks. Such frameworks typically use spherical harmonics as angular basis functions, followed by Clebsch-Gordan contraction to maintain rotational symmetry. We propose a mathematically equivalent and simple alternative that performs all operations in the Cartesian coordinates. This approach provides a complete set of polynormially independent features of atomic environments while maintaining interaction body orders. Additionally, we integrate low-dimensional embeddings of various chemical elements, trainable radial channel coupling, and inter-atomic message passing. The resulting potential, named Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability, and generalizability. We validate its performance in diverse systems, including bulk water, small molecules, and 25-element high-entropy alloys. [ABSTRACT FROM AUTHOR]

Proton hopping is a key reactive process within zeolite catalysis. However, the accurate determination of its kinetics poses major challenges both for theoreticians and experimentalists. Nuclear quantum effects (NQEs) are known to influence the structure and dynamics of protons, but their rigorous inclusion through the path integral molecular dynamics (PIMD) formalism was so far beyond reach for zeolite catalyzed processes due to the excessive computational cost of evaluating all forces and energies at the Density Functional Theory (DFT) level. Herein, we overcome this limitation by training first a reactive machine learning potential (MLP) that can reproduce with high fidelity the DFT potential energy surface of proton hopping around the first Al coordination sphere in the H-CHA zeolite. The MLP offers an immense computational speedup, enabling us to derive accurate reaction kinetics beyond standard transition state theory for the proton hopping reaction. Overall, more than 0.6 μs of simulation time was needed, which is far beyond reach of any standard DFT approach. NQEs are found to significantly impact the proton hopping kinetics up to ~473 K. Moreover, PIMD simulations with deuterium can be performed without any additional training to compute kinetic isotope effects over a broad range of temperatures., (© 2023. The Author(s).)

In this analysis, nanofluid properties are evaluated by interaction correlations between particles using molecular dynamics (MD) method, and thermal-hydraulics characteristics of nanofluids in a WWER-1000 reactor is investigated by Computational Fluid Dynamics (CFD). This study conceptualizes power increase by changing the cooling from pure water to nanofluid without changing the safety parameters. The Copper nanoparticles are used in primary loop cooling system, to evaluate the heat removal from the core. Thermophysical properties such as thermal conductivity and shear viscosity of Cu-Water nanofluids are obtained by MD in operating pressure and temperature of the Bushehr reactor core. These properties have been used in thermal-hydraulics analysis and nanofluids are considered as a homogeneous fluid. Thermal hydraulic properties of coolant have been calculated for different volume fractions of nanofluids. Thermal hydraulic simulation illustrated enhancement of the thermal characteristics of the core, due to the increment in heat transfer coefficient and thermal diffusivity. The thermal-hydraulic analysis of the reactor core has been performed in steady state at different powers. The requirements for changing the reactor power are not to change the fuel center temperature and Outer Cladding Surface temperature compared to the current state. [ABSTRACT FROM AUTHOR]

Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the chemical and morphological complexity of glasses calls for atomistic simulations where the interatomic potentials are able to capture the variety of local environments, composition, and (dis)order that typically characterize glassy phases. Machine-learning potentials (MLPs) are emerging as a valid alternative to computationally expensive ab initio simulations, inevitably run on very small samples which cannot account for disorder at different scales, as well as to empirical force fields, fast but often reliable only in a narrow portion of the thermodynamic and composition phase diagrams. In this article, we make the point on the use of MLPs to compute the thermal conductivity of glasses, through a review of recent theoretical and computational tools and a series of numerical applications on vitreous silica and vitreous silicon, both pure and intercalated with lithium. [ABSTRACT FROM AUTHOR]

The fullerene-like structures can be characterized not only by the classical topology (12 pentagonal and rest hexagonal rings), but can also contain 4-membered rings (typically forbidden due to strong steric stresses). Here we report the numbers and the symmetry point group statistics for all C20–C60 fulleroids with 4-membered rings (141325 in total). The most symmetrical structures with 6 to 120 automorphism group orders (251 in total) are drawn in Schlegel diagrams and characterized by facet sets and symmetry point groups in the list. Among them, 19 series of tubulen-like structures constructed from pairs of the same caps separated by belts of hexagons have been found. The obtained results are of practical interest and can be used for the description of the topologies of polyoxometallates with the fullerene-related structures. [ABSTRACT FROM AUTHOR]

Magnetoreception, the remarkable ability of organisms to perceive and respond to Earth's magnetic field, has captivated scientists for decades, particularly within the field of quantum biology. In the plant science, the exploration of the complicated interplay between quantum phenomena and classical biology in the context of plant magnetoreception has emerged as an attractive area of research. This comprehensive review investigates into three prominent theoretical models: the Radical Pair Mechanism (RPM), the Level Crossing Mechanism (LCM), and the Magnetite-based MagR theory in plants. While examining the advantages, limitations, and challenges associated with each model, this review places a particular weight on the RPM, highlighting its wellestablished role of cryptochromes and in-vivo experiments on light-independent plant magnetoreception. However, alternative mechanisms such as the LCM and the MagR theory are objectively presented as convincing perspectives that permit further investigation. To shed light on these theoretical frameworks, this review proposes experimental approaches including cutting-edge experimental techniques. By integrating these approaches, a comprehensive understanding of the complex mechanisms driving plant magnetoreception can be achieved, lending support to the fundamental principle in the RPM. In conclusion, this review provides a panoramic overview of plant magnetoreception, highlighting the exciting potential of quantum biology in unraveling the mysteries of magnetoreception. As researchers embark on this captivating scientific journey, the doors to decipher ing the diverse mechanisms of magnetoreception in plants stand wide open, offering a profound exploration of nature's adaptations to environmental cues. [ABSTRACT FROM AUTHOR]