Controlling the charge-transfer dynamics of two-level systems around avoided crossings.

Two-level quantum systems are fundamental physical models that continue to attract growing interest due to their crucial role as a building block of quantum technologies. The exact analytical solution of the dynamics of these systems is central to control theory and its applications, such as that to quantum computing. In this study, we reconsider the two-state charge transfer problem by extending and using a methodology developed to study (pseudo)spin systems in quantum electrodynamics contexts.

Unraveling the electronic origin of a special feature in the triplet-minus-singlet spectra of carotenoids in natural photosystems.

The influence of carotenoid triplet states on the Q electronic transitions of chlorophylls has been observed in experiments on light-harvesting complexes over the past three decades, but the interpretation of the resulting spectral feature in the triplet minus singlet (T-S) absorption spectra of photosystems is still debated, as the physical-chemical explanation of this feature has been elusive. Here, we resolve this debate, by explaining the T-S spectra of pigment complexes over the Q-band spectral region through a comparative study of chlorophyll-carotenoid model dyads and larger pigment complexes from the main light harvesting complex of higher plants (LHCII). This goal is achieved by combining state-of-the-art time-dependent density functional theory with analysis of the relationship between electronic properties and nuclear structure, and by comparison to the experiment.

Quantum-Classical Hybrid Systems and Ehrenfest's Theorem.

The conceptual analysis of quantum mechanics brings to light that a theory inherently consistent with observations should be able to describe both quantum and classical systems, i.e., quantum-classical hybrids.

Adenine Fine-Tunes DNA Photolyase's Repair Mechanism.

The comparative study of DNA repair by mesophilic and extremophilic photolyases helps us understand the evolution of these enzymes and their role in preserving life on our changing planet. The mechanism of repair of cyclobutane pyrimidine dimer lesions in DNA by electron transfer from the flavin adenine dinucleotide cofactor is the subject of intense interest. The role of adenine in mediating this process remains unresolved.

Hermitian and Unitary Almost-Companion Matrices of Polynomials on Demand.

We introduce the concept of the almost-companion matrix (ACM) by relaxing the non-derogatory property of the standard companion matrix (CM). That is, we define an ACM as a matrix whose characteristic polynomial coincides with a given monic and generally complex polynomial. The greater flexibility inherent in the ACM concept, compared to CM, allows the construction of ACMs that have convenient matrix structures satisfying desired additional conditions, compatibly with specific properties of the polynomial coefficients.

Invariant-Parameterized Exact Evolution Operator for (2) Systems with Time-Dependent Hamiltonian.

We report the step-by-step construction of the exact, closed and explicit expression for the evolution operator U(t) of a localized and isolated qubit in an arbitrary time-dependent field, which for concreteness we assume to be a magnetic field. Our approach is based on the existence of two independent dynamical invariants that enter the expression of SU(2) by means of two strictly related time-dependent, real or complex, parameters. The usefulness of our approach is demonstrated by exactly solving the quantum dynamics of a qubit subject to a controllable time-dependent field that can be realized in the laboratory.

Symmetry-Induced Emergence of a Pseudo-Qutrit in the Dipolar Coupling of Two Qubits.

We investigate a system of two identical and distinguishable spins 1/2, with a direct magnetic dipole-dipole interaction, in an external magnetic field. Constraining the hyperfine tensor to exhibit axial symmetry generates the notable symmetry properties of the corresponding Hamiltonian model. In fact, we show that the reduction of the anisotropy induces the invariance of the Hamiltonian in the 3×3 subspace of the Hilbert space of the two spins in which S^2 invariably assumes its highest eigenvalue of 2.

Mechanism of Side Chain-Controlled Proton Conductivity in Bioinspired Peptidic Nanostructures.

Bioinspired peptide assemblies are promising candidates for use as proton-conducting materials in electrochemical devices and other advanced technologies. Progress toward applications requires establishing foundational structure-function relationships for transport in these materials. This experimental-theoretical study sheds light on how the molecular structure and proton conduction are linked in three synthetic cyclic peptide nanotube assemblies that comprise the three canonical basic amino acids (lysine, arginine, and histidine).

Temperature Dependence of Charge and Spin Transfer in Azurin.

The steady-state charge and spin transfer yields were measured for three different Ru-modified azurin derivatives in protein films on silver electrodes. While the charge-transfer yields exhibit weak temperature dependences, consistent with operation of a near activation-less mechanism, the spin selectivity of the electron transfer improves as temperature increases. This enhancement of spin selectivity with temperature is explained by a vibrationally induced spin exchange interaction between the Cu(II) and its chiral ligands.

Correlation between Charge Transport and Base Excision Repair in the MutY-DNA Glycosylase.

Experimental evidence suggests that DNA-mediated redox signaling between high-potential [FeS] proteins is relevant to DNA replication and repair processes, and protein-mediated charge transfer (CT) between [FeS] clusters and nucleic acids is a fundamental process of the signaling and repair mechanisms. We analyzed the dominant CT pathways in the base excision repair glycosylase MutY using molecular dynamics simulations and hole hopping pathway analysis. We find that the adenine nucleobase of the mismatched A·oxoG DNA base pair facilitates [FeS]-DNA CT prior to adenine excision by MutY.

Mutation effects on charge transport through the p58c iron-sulfur protein.

Growing experimental evidence indicates that iron-sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [FeS] clusters, mediated by proteins and DNA, may convey signals to coordinate enzyme action. Human primase is a well studied [FeS] protein, and its p58c domain (which contains an [FeS] cluster) plays a role in the initiation of DNA replication.

Electrostatic Field-Induced Oscillator Strength Focusing in Molecules.

The development of light-harvesting devices based on molecular materials depends critically on the ability to focus the electronic oscillator strength of molecules into the UV-vis spectral window. Typical molecular chromophores have only about 1% of their total electronic oscillator strength in this spectral region and thus perform at a small fraction of their possible effectiveness. This theoretical study finds that the electronic oscillator strength of polyenes in the UV-vis region may be enhanced by 1 order of magnitude using electrostatic fields, motivating specific experimental studies of oscillator strength focusing.

2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport.

The non-biological 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2'F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2'F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs.

Correction: Charge Transfer between [4Fe4S] Proteins and DNA Is Unidirectional: Implications for Biomolecular Signaling.

[This corrects the article PMC6350243.].

Mapping hole hopping escape routes in proteins.

A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on the mean residence times of the transferring charge along these hopping pathways. The residence times are estimated by combining a kinetic model with well-known rate expressions for the charge-transfer steps in the pathways.

How To Extract Quantitative Information on Electronic Transitions from the Density Functional Theory "Black Box".

Electronic couplings and vertical excitation energies are crucial determinants of charge and excitation energy transfer rates in a broad variety of processes ranging from biological charge transfer to charge transport through inorganic materials, from molecular sensing to intracellular signaling. Density Functional Theory (DFT) is generally used to calculate these critical parameters, but the quality of the results is unpredictable because of the semiempirical nature of the available DFT approaches. This study identifies a small set of fundamental rules that enables accurate DFT computation of electronic couplings and vertical excitation energies in molecular complexes and materials.

Charge Transfer between [4Fe4S] Proteins and DNA Is Unidirectional: Implications for Biomolecular Signaling.

Recent experiments suggest that DNA-mediated charge transport might enable signaling between the [4Fe4S] clusters in the C-terminal domains of human DNA primase and polymerase α, as well as the signaling between other replication and repair high-potential [4Fe4S] proteins. Our theoretical study demonstrates that the redox signaling cannot be accomplished exclusively by DNA-mediated charge transport because part of the charge transfer chain has an unfavorable free energy profile. We show that hole or excess electron transfer between a [4Fe4S] cluster and a nucleic acid duplex through a protein medium can occur within microseconds in one direction, while it is kinetically hindered in the opposite direction.

A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation.

Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function.

Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability.

The non-biological nucleic acid 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be of use because of its higher chemical stability than DNA in terms of resistance to hydrolysis and nuclease degradation. In order to investigate the charge transfer characteristics of 2'F-ANA, of relevance to applications in nucleic acid-based biosensors and chip technologies, we compare the electronic couplings for hole transfer between stacked nucleobase pairs in DNA and 2'F-ANA by carrying out density functional theory (DFT) calculations on geometries taken from molecular dynamics simulations. We find similar averages and distribution widths of the base-pair couplings in the two systems.

Determinants of Photolyase's DNA Repair Mechanism in Mesophiles and Extremophiles.

Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood.

Covalently bonded single-molecule junctions with stable and reversible photoswitched conductivity.

Through molecular engineering, single diarylethenes were covalently sandwiched between graphene electrodes to form stable molecular conduction junctions. Our experimental and theoretical studies of these junctions consistently show and interpret reversible conductance photoswitching at room temperature and stochastic switching between different conductive states at low temperature at a single-molecule level. We demonstrate a fully reversible, two-mode, single-molecule electrical switch with unprecedented levels of accuracy (on/off ratio of ~100), stability (over a year), and reproducibility (46 devices with more than 100 cycles for photoswitching and ~10(5) to 10(6) cycles for stochastic switching).

Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra.

The effectiveness of solar energy capture and conversion materials derives from their ability to absorb light and to transform the excitation energy into energy stored in free carriers or chemical bonds. The Thomas-Reiche-Kuhn (TRK) sum rule mandates that the integrated (electronic) oscillator strength of an absorber equals the total number of electrons in the structure. Typical molecular chromophores place only about 1% of their oscillator strength in the UV-vis window, so individual chromophores operate at about 1% of their theoretical limit.

Sensing of molecules using quantum dynamics.

We design sensors where information is transferred between the sensing event and the actuator via quantum relaxation processes, through distances of a few nanometers. We thus explore the possibility of sensing using intrinsically quantum mechanical phenomena that are also at play in photobiology, bioenergetics, and information processing. Specifically, we analyze schemes for sensing based on charge transfer and polarization (electronic relaxation) processes.

Long-range charge transport in single G-quadruplex DNA molecules.

DNA and DNA-based polymers are of interest in molecular electronics because of their versatile and programmable structures. However, transport measurements have produced a range of seemingly contradictory results due to differences in the measured molecules and experimental set-ups, and transporting significant current through individual DNA-based molecules remains a considerable challenge. Here, we report reproducible charge transport in guanine-quadruplex (G4) DNA molecules adsorbed on a mica substrate.