A novel non-adiabatic spin relaxation mechanism in molecular qubits.

The interaction of electronic spin and molecular vibrations mediated by spin-orbit coupling governs spin relaxation in molecular qubits. We derive an extended molecular spin Hamiltonian that includes both adiabatic and non-adiabatic spin-dependent interactions, and we implement the computation of its matrix elements using state-of-the-art density functional theory. The new molecular spin Hamiltonian contains a novel spin-vibrational orbit interaction with a non-adiabatic origin, together with the traditional molecular Zeeman and zero-field splitting interactions with an adiabatic origin.

Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data.

Microcanonical rates from ring-polymer molecular dynamics: Direct-shooting, stationary-phase, and maximum-entropy approaches.

We address the calculation of microcanonical reaction rates for processes involving significant nuclear quantum effects using ring-polymer molecular dynamics (RPMD), both with and without electronically non-adiabatic transitions. After illustrating the shortcomings of the naive free-particle direct-shooting method, in which the temperature of the internal ring-polymer modes is set to the translational energy scale, we investigate alternative strategies based on the expression for the microcanonical rate in terms of the inverse Laplace transform of the thermal reaction rate. It is shown that simple application of the stationary-phase approximation (SPA) dramatically improves the performance of the microcanonical rates using RPMD, particularly in the low-energy region where tunneling dominates.

Real-time density-matrix coupled-cluster approach for closed and open systems at finite temperature.

We extend the coupled-cluster method to correlated quantum dynamics of both closed and open systems at finite temperatures using the thermofield formalism. The approach expresses the time-dependent density matrix in an exponential ansatz and describes time-evolution along the Keldysh path contour. A distinct advantage of the approach is exact trace-preservation as a function of time, ensuring conservation of probability and particle number.

Publisher Correction: Direct dioxygen evolution in collisions of carbon dioxide with surfaces.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Direct dioxygen evolution in collisions of carbon dioxide with surfaces.

The intramolecular conversion of CO to molecular oxygen is an exotic reaction, rarely observed even with extreme optical or electronic excitation means. Here we show that this reaction occurs readily when CO ions scatter from solid surfaces in a two-step sequential collision process at hyperthermal incidence energies. The produced O is preferentially ionized by charge transfer from the surface over the predominant atomic oxygen product, leading to direct detection of both O and O.

Simple Flux-Side Formulation of State-Resolved Thermal Reaction Rates for Ring-Polymer Surface Hopping.

Employing the recently developed isomorphic Hamiltonian framework for including nuclear quantum effects in mixed quantum-classical nonadiabatic dynamics, we present a flux-side formulation of state-resolved thermal reaction rates for ring-polymer surface hopping (iso-RPSH). An appealing aspect of the new approach is that calculation of multiple state-resolved nonadiabatic thermal reaction rates is enabled with only a single free-energy surface calculation, whereas previous nonadiabatic flux-side formulations for surface hopping involve multiple free-energy surface calculations. The method is shown to be robust and straightforwardly implemented, and numerical results reveal that RPSH in the isomorphic Hamiltonian framework leads to better dividing surface independence than alternative RPSH methods due to improved preservation of the path-integral statistics.

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity.

The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research.

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics.

We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation.

A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1-86).

We propose a novel, special purpose semiempirical tight binding (TB) method for the calculation of structures, vibrational frequencies, and noncovalent interactions of large molecular systems with 1000 or more atoms. The functional form of the method is related to the self-consistent density functional TB scheme and mostly avoids element-pair-specific parameters. The parametrization covers all spd-block elements and the lanthanides up to Z = 86 using reference data at the hybrid density functional theory level.

Synthesis and Dynamics of Nanosized Phenylene-Ethynylene-Butadiynylene Rotaxanes and the Role of Shape Persistence.

Phenylacetylene-based [2]rotaxanes were synthesized by a covalent-template approach by aminolysis of the corresponding prerotaxanes. The wheel and the bulky stoppers are made of phenylene-ethynylene-butadiynylene macrocycles of the same size. The stoppers are large enough to enable the synthesis and purification of the rotaxane.

On the connection of semiclassical instanton theory with Marcus theory for electron transfer in solution.

We present a derivation of Marcus theory of electron transfer in solution starting from semiclassical instanton theory. The conventional semiclassical instanton theory provides an inadequate description of the electron transfer process in the inverted Marcus regime. This has been attributed to the lack of backscattering in the product region, which is represented as a semi-infinite continuum of states.

Orthogonality constrained density functional theory for electronic excited states.

We report a novel scheme for computing electronic excitation energies within the framework of density functional theory (DFT) based on a time-independent variational formulation of DFT. The excited state density functional is recast as a Kohn-Sham functional, which is further simplified by an adiabatic approximation of the exchange-correlation functional. Under the adiabatic approximation, the minimization of the excited state Kohn-Sham functional is shown to be equivalent to a ground state DFT computation augmented with orthogonality constraints with respect to the ground state Kohn-Sham determinant.

Ring polymer molecular dynamics with surface hopping.

We propose a ring polymer molecular dynamics method for the calculation of chemical rate constants that incorporates nonadiabatic effects by the surface-hopping approach. Two approximate ring polymer electronic Hamiltonians are formulated and the time-dependent Schrodinger equation for the electronic amplitudes is solved self-consistently with the ring polymer equations of motion. The beads of the ring polymer move on a single adiabatic potential energy surface at all times except for instantaneous surface hops.

Mixed time slicing in path integral simulations.

A simple and efficient scheme is presented for using different time slices for different degrees of freedom in path integral calculations. This method bridges the gap between full quantization and the standard mixed quantum-classical (MQC) scheme and, therefore, still provides quantum mechanical effects in the less-quantized variables. Underlying the algorithm is the notion that time slices (beads) may be "collapsed" in a manner that preserves quantization in the less quantum mechanical degrees of freedom.

Molecular dynamics study of the electric and dielectric properties of model DPPC and dicaprin insoluble monolayers: size effect.

Atomistic modeling of insoluble monolayers is currently used to inspect their organization and electric characteristics, providing a link between theory and experiment. Extensive molecular dynamics simulations at 300 K were carried out for model films of the lipids dipalmitoylphosphatidylcholine (DPPC) and dicaprin (DC) at the air/water interface. Surface concentrations corresponding to a set of points along the surface pressure/area isotherms of the surfactants were considered.

Structural aspects of lipid monolayers: computer simulation analyses.

Extensive molecular dynamics simulations at room temperature were carried out for model films of two dissimilar lipids (DPPC and dicaprin) at the air/water interface. To study the peculiarities of the organization patterns at different average areas per molecule, surface concentrations corresponding to five almost equally spaced points along the isotherms of the two surfactants were considered. A variable of prime interest was the density distribution in a direction normal to the interface of the monolayer components: interfacial water and surfactant on one hand and the separate moieties of the lipids on the other hand.

Systematic study of the influence of base-step parameters on the electronic coupling between base-pair dimers: comparison of A-DNA and B-DNA forms.

The electronic coupling is one of the key parameters governing electron hole transfer along DNA helices. In this study, we established the first comprehensive data base of electronic coupling elements, calculated at the ab initio level. The data set comprises all possible Watson-Crick base pair dimers, both in standard A-DNA and B-DNA geometries.

Dielectric properties tangential to the interface in model insoluble monolayers: theoretical assessment.

Studies of insoluble monolayers built of phospholipids and various long-chained fatty acids or their glycerin esters are the major source for what is currently known about the relationship between monolayer composition and physicochemical properties. The surface pressure, dipole moment, dielectric permittivity, polarizability, refractivity, and other electrical and optical features are governed by the surfactant structural specificity and solvent organization at the microscopic level. To provide insight into the atomistic details of the interfacial structure, model monolayers at the air/water interface of two distinctly different in composition and isotherm profile surfactants are investigated by means of molecular dynamics all-atom simulations.