Electronic Coherences Excited by an Ultra Short Pulse Are Robust with Respect to Averaging over Randomly Oriented Molecules as Shown by Singular Value Decomposition.

We report a methodology for averaging quantum photoexcitation vibronic dynamics over the initial orientations of the molecules with respect to an ultrashort light pulse. We use singular value decomposition of the ensemble density matrix of the excited molecules, which allows the identification of the few dominant principal molecular orientations with respect to the polarization direction of the electric field. The principal orientations provide insights into the specific stereodynamics of the corresponding principal molecular vibronic states. The massive compaction of the vibronic density matrix of the ensemble of randomly oriented pumped molecules enables a most efficient fully quantum mechanical time propagation scheme. Two examples are discussed for the quantum dynamics of the LiH molecule in the manifolds of its electronically excited Σ and Π states. Our results show that electronic and vibrational coherences between excited states of the same symmetry are resilient to averaging over an ensemble of molecular orientations and can be selectively excited at the ensemble level by tuning the pulse parameters.

Nonadiabatic quantum dynamics explores non-monotonic photodissociation branching of N2 into the N(4S) + N(2D) and N(4S) + N(2P) product channels.

Vacuum ultraviolet (VUV) photodissociation of N2 molecules is a source of reactive N atoms in the interstellar medium. In the energy range of VUV optical excitation of N2, the N-N triple bond cleavage leads to three types of atoms: ground-state N(4S) and excited-state N(2P) and N(2D). The latter is the highest reactive and it is believed to be the primary participant in reactions with hydrocarbons in Titan's atmosphere. Experimental studies have observed a non-monotonic energy dependence and non-statistical character of the photodissociation of N2. This implies different dissociation pathways and final atomic products for different wavelength regions in the sunlight spectrum. We here apply ab initio quantum chemical and nonadiabatic quantum dynamical techniques to follow the path of an electronic state from the excitation of a particular singlet 1Σ+u and 1Πu vibronic level of N2 to its dissociation into different atomic products. We simulate dynamics for two isotopomers of the nitrogen molecule, 14N2 and 14N15N for which experimental data on the branching are available. Our computations capture the non-monotonic energy dependence of the photodissociation branching ratios in the energy range 108 000-116 000 cm-1. Tracing the quantum dynamics in a bunch of electronic states enables us to identify the key components that determine the efficacy of singlet to triplet population transfer and therefore predissociation lifetimes and branching ratios for different energy regions.

Time-Frequency Signatures of Electronic Coherence of Colloidal CdSe Quantum Dot Dimer Assemblies Probed at Room Temperature by Two-Dimensional Electronic Spectroscopy.

Electronic coherence signatures can be directly identified in the time-frequency maps measured in two-dimensional electronic spectroscopy (2DES). Here, we demonstrate the theory and discuss the advantages of this approach via the detailed application to the fast-femtosecond beatings of a wide variety of electronic coherences in ensemble dimers of quantum dots (QDs), assembled from QDs of 3 nm in diameter, with 8% size dispersion in diameter. The observed and computed results can be consistently characterized directly in the time-frequency domain by probing the polarization in the 2DES setup. The experimental and computed time-frequency maps are found in very good agreement, and several electronic coherences are characterized at room temperature in solution, before the extensive dephasing due to the size dispersion begins. As compared to the frequency-frequency maps that are commonly used in 2DES, the time-frequency maps allow exploiting electronic coherences without additional post-processing and with fewer 2DES measurements. Towards quantum technology applications, we also report on the modeling of the time-frequency photocurrent response of these electronic coherences, which paves the way to integrating QD devices with classical architectures, thereby enhancing the quantum advantage of such technologies for parallel information processing at room temperature.

Recombination of N Atoms in a Manifold of Electronic States Simulated by Time-Reversed Nonadiabatic Photodissociation Dynamics of N2.

Following a single photon VUV absorption, the N2 molecule dissociates into distinct channels leading to N atoms of different reactivities. The optically accessible singlets are bound, and dissociation occurs through spin-orbit induced transfer to the triplets. There is a forest of coupled electronic states, and we here aim to trace a path along the nonadiabatic couplings toward a particular exit channel. To achieve this, we apply a time-reversed quantum dynamical approach that corresponds to a dissociation running back. It begins with an atom-atom relative motion in a particular product channel. Starting with a Gaussian wave packet at the dissociation region of N2 and propagating it backward in time, one can see the population transferring among the triplets due to a strong nonadiabatic interaction between these states. Simultaneously, the optically active singlets get populated because of spin-orbit coupling to the triplets. Thus, backward propagation traces the nonradiative association of nitrogen atoms.

Nonadiabatic dynamics in a forest of coupled states: Electronic state branching in the VUV photodissociation of N2.

Multi-state electronic dynamics at higher excitation energies is needed for the understanding of a variety of energy rich situations, including chemistry under extreme conditions, vacuum ultraviolet (VUV) induced astrochemistry, and attochemistry. It calls for an understanding of three stages, energy acquisition, dynamical propagation, and disposal. It is typically not possible to identify a basis of uncoupled quantum states that is sufficient for the three stages. The handicap is the large number of coupled quantum states that is needed to describe the system. Progress in quantum chemistry provides the necessary background to the energetics and the coupling. Progress in quantum dynamics takes this as input for the propagation in time. Right now, it seems that we have come of age with potential detailed applications. We here report a demonstration to a coupled electron-nuclear quantum dynamics through a maze of 47 electronic states and with attention to the order in perturbation theory that is indicated using propensity rules for couplings. Close agreement with experimental results for the VUV photodissociation of 14N2 and its isotopomer 14N15N is achieved. We pay special attention to the coupling between two dissociative continua and an optically accessible bound domain. The computations reproduce and interpret the non-monotonic branching between the two exit channels producing N(2D) and N(2P) atoms as a function of excitation energy and its variation with the mass.

Correction: Bond breaking of furan-maleimide adducts via a diradical sequential mechanism under an external mechanical force.

[This corrects the article DOI: 10.1039/D2SC05051J.].

Bond breaking of furan-maleimide adducts via a diradical sequential mechanism under an external mechanical force.

Substituted furan-maleimide Diels-Alder adducts are bound by dynamic covalent bonds that make them particularly attractive mechanophores. Thermally activated [4 + 2] retro-Diels-Alder (DA) reactions predominantly proceed via a concerted mechanism in the ground electronic state. We show that an asymmetric mechanical force along the anchoring bonds in both the endo and exo isomers of proximal dimethyl furan-maleimide adducts favors a sequential pathway. The switching from a concerted to a sequential mechanism occurs at external forces of ≈1 nN. The first bond rupture occurs for a projection of the pulling force on the scissile bond at ≈4.3 nN for the exo adduct and ≈3.8 nN for the endo one. The reaction is inhibited for external forces up to ≈3.4 nN for the endo adduct and 3.6 nN for the exo one after which it is activated. In the activated region, at 4 nN, the rupture rate of the first bond for the endo adduct is computed to be ≈3 orders of magnitude larger than for the exo one in qualitative agreement with recent sonication experiments [Z. Wang and S. L. Craig, Chem. Commun., 2019, 55, 12263-12266]. In the intermediate region of the path between the rupture of the first and the second bond, the lowest singlet state exhibits a diradical character for both adducts and is close in energy to a diradical triplet state. The computed values of spin-orbit coupling along the path are too small for inducing intersystem crossings. These findings open the way for the rational design of DA mechanophores for polymer science and photochemistry.

Few-Femtosecond C2H4+ Internal Relaxation Dynamics Accessed by Selective Excitation.

Dissociation of the ethylene cation is a prototypical multistep pathway in which the exact mechanisms leading to internal energy conversions are not fully known. For example, it is still unclear how the energy is exactly redistributed among the internal modes and which step is rate-determining. Here we use few-femtosecond extreme-ultraviolet pulses of tunable energy to excite a different superposition of the four lowest states of C2H4+ and probe the subsequent fast relaxation with a short infrared pulse. Our results demonstrate that the infrared pulse photoexcites the cationic ground state (GS) to higher excited states, producing a hot GS upon relaxation, which enhances the fragmentation yield. As the photoexcitation probability of the GS strongly depends on the molecular geometry, the probing by the IR pulse provides information about the ultrafast excited-state dynamics and the type of conical intersection (planar or twisted) involved in the first 20 fs of the nonradiative relaxation.

Compacting the density matrix in quantum dynamics: Singular value decomposition of the surprisal and the dominant constraints for anharmonic systems.

We introduce a practical method for compacting the time evolution of the quantum state of a closed physical system. The density matrix is specified as a function of a few time-independent observables where their coefficients are time-dependent. The key mathematical step is the vectorization of the surprisal, the logarithm of the density matrix, at each time point of interest. The time span used depends on the required spectral resolution. The entire course of the system evolution is represented as a matrix where each column is the vectorized surprisal at the given time point. Using the singular value decomposition (SVD) of this matrix, we generate realistic approximations for the time-independent observables and their respective time-dependent coefficients. This allows for a simplification of the algebraic procedure for determining the dominant constraints (the time-independent observables) in the sense of the maximal entropy approach. A non-stationary coherent initial state of a Morse oscillator is used to introduce the approach. We derive the analytical exact expression for the surprisal as a function of time, and this offers a benchmark for comparison with the accurate but approximate SVD results. We discuss two examples of a Morse potential of different anharmonicities, H2 and I2 molecules. We further demonstrate the approach for a two-coupled electronic state problem, the well-studied non-radiative decay of pyrazine from its bright state. Five constraints are found to be enough to capture the ultrafast electronic population exchange and to recover the dynamics of the wave packet in both electronic states.

Ellipticity controlled dissociative double ionization of ethane by strong fields.

The yields of all dissociation channels of ethane dications produced by strong field double ionization were measured. It was found that the branching ratios can be controlled by varying the ellipticity of laser pulses. The CH3+ formation and H+ formation channels show a clear competition, producing the highest and lowest branching ratios at ellipticity of ∼0.6, respectively. With the help of theoretical calculations, such a control was attributed to the ellipticity dependent yields of different sequential ionization pathways.

Identification of an ultrafast internal conversion pathway of pyrazine by time-resolved vacuum ultraviolet photoelectron spectrum simulations.

The internal conversion from the optically bright S2 (1B2u, ππ*) state to the dark S1 (1B3u, nπ*) state in pyrazine is a standard benchmark for experimental and theoretical studies on ultrafast radiationless decay. Since 2008, a few theoretical groups have suggested significant contributions of other dark states S3 (1Au, nπ*) and S4 (1B2g, nπ*) to the decay of S2. We have previously reported the results of nuclear wave packet simulations [Kanno et al., Phys. Chem. Chem. Phys. 17, 2012 (2015)] and photoelectron spectrum calculations [Mignolet et al., Chem. Phys. 515, 704 (2018)] that support the conventional two-state picture. In this article, the two different approaches, i.e., wave packet simulation and photoelectron spectrum calculation, are combined: We computed the time-resolved vacuum ultraviolet photoelectron spectrum and photoelectron angular distribution for the ionization of the wave packet transferred from S2 to S1. The present results reproduce almost all the characteristic features of the corresponding experimental time-resolved spectrum [Horio et al., J. Chem. Phys. 145, 044306 (2016)], such as a rapid change from a three-band to two-band structure. This further supports the existence and character of the widely accepted pathway (S2 → S1) of ultrafast internal conversion in pyrazine.

DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations.

A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.

Thermodynamic energetics underlying genomic instability and whole-genome doubling in cancer.

Genomic instability contributes to tumorigenesis through the amplification and deletion of cancer driver genes. DNA copy number (CN) profiling of ensembles of tumors allows a thermodynamic analysis of the profile for each tumor. The free energy of the distribution of CNs is found to be a monotonically increasing function of the average chromosomal ploidy. The dependence is universal across several cancer types. Surprisal analysis distinguishes two main known subgroups: tumors with cells that have or have not undergone whole-genome duplication (WGD). The analysis uncovers that CN states having a narrower distribution are energetically more favorable toward the WGD transition. Surprisal analysis also determines the deviations from a fully stable-state distribution. These deviations reflect constraints imposed by tumor fitness selection pressures. The results point to CN changes that are more common in high-ploidy tumors and thus support altered selection pressures upon WGD.

Metabolic, Physiological, and Transcriptomics Analysis of Batch Cultures of the Green Microalga Chlamydomonas Grown on Different Acetate Concentrations.

Acetate can be efficiently metabolized by the green microalga Chlamydomonasreinhardtii. The regular concentration is 17 mM, although higher concentrations are reported to increase starch and fatty acid content. To understand the responses to higher acetate concentrations, Chlamydomonas cells were cultivated in batch mode in the light at 17, 31, 44, and 57 mM acetate. Metabolic analyses show that cells grown at 57 mM acetate possess increased contents of all components analyzed (starch, chlorophylls, fatty acids, and proteins), with a three-fold increased volumetric biomass yield compared to cells cultivated at 17 mM acetate at the entry of stationary phase. Physiological analyses highlight the importance of photosynthesis for the low-acetate and exponential-phase samples. The stationary phase is reached when acetate is depleted, except for the cells grown at 57 mM acetate, which still divide until ammonium exhaustion. Surprisal analysis of the transcriptomics data supports the biological significance of our experiments. This allows the establishment of a model for acetate assimilation, its transcriptional regulation and the identification of candidates for genetic engineering of this metabolic pathway. Altogether, our analyses suggest that growing at high-acetate concentrations could increase biomass productivities in low-light and CO2-limiting air-bubbled medium for biotechnology.

Time resolved mechanism of the isotope selectivity in the ultrafast light induced dissociation in N2.

The time evolution of a vacuum ultraviolet excited N2 molecule is followed all the way from an ultrafast excitation to dissociation by a quantum mechanical simulation. The primary aim is to discern the role of the excitation by a pulse short compared to the vibrational period, to discern the different coupling mechanisms between different electronic states, nonadiabatic, spin orbit, and to analyze the origin of any isotopic effect. We compare the picture in the time and energy domains. The initial ultrafast excitation pumps the molecule to a coherent electronic wave packet to which several singlet bound electronic states contribute. The total nonstationary wave function is given as a coherent sum of nuclear wave packets on each electronic state times the stationary electronic wave function. When the wave packets on different electronic states overlap, they are coupled in a mass-dependent manner whether one uses an adiabatic or a diabatic electronic basis. A weak spin-orbit coupling acts as a bottleneck between the bound singlet part of phase space and the triplet manifold of states in which dissociation takes place. To describe the spin-orbit perturbation that is ongoing in time, an energy-resolved eigenstate representation appears to be more intuitive. In the eigenstate basis, the singlet-to-triplet population transfer is large only between those vibronic eigenstates that are quasiresonant in energy. The states in resonance are different for different excitation energy ranges. The resonances are mass dependent, which explains the control of the isotope effect through the profile of the pulse.

Intracellular redox potential is correlated with miRNA expression in MCF7 cells under hypoxic conditions.

Hypoxia is a ubiquitous feature of cancers, encouraging glycolytic metabolism, proliferation, and resistance to therapy. Nonetheless, hypoxia is a poorly defined term with confounding features described in the literature. Redox biology provides an important link between the external cellular microenvironment and the cell's response to changing oxygen pressures. In this paper, we demonstrate a correlation between intracellular redox potential (measured using optical nanosensors) and the concentrations of microRNAs (miRNAs) involved in the cell's response to changes in oxygen pressure. The correlations were established using surprisal analysis (an approach derived from thermodynamics and information theory). We found that measured redox potential changes reflect changes in the free energy computed by surprisal analysis of miRNAs. Furthermore, surprisal analysis identified groups of miRNAs, functionally related to changes in proliferation and metastatic potential that played the most significant role in the cell's response to changing oxygen pressure.

Understanding chemical interaction between phosphonate-derivative molecules and a silver surface cluster in SERS: a combined experimental and computational approach.

The interaction between phosphonate functions and a silver surface cluster is investigated using Surface-Enhanced Raman Spectroscopy (SERS). Changing the functional group (methylphosphonic acid based molecule) by studying the effect of protonation, methylation and substitution of the side chain with amine and carboxylate functions enabled us to modulate the chemical interactions between the different functions and the metal cluster. We find that the adsorption energy of the methylphosphonic acid decreases with the protonation, the methylation processes and the substitution of the side chain. In all cases, only the deprotonated phosphonate forms are SERS active. To understand how the molecules interact with the nanoparticle, the electronic structure, adsorption energies and Raman spectra were computed for molecules adsorbed on a 20 atom silver cluster representing a nanoparticle surface. The qualitative agreement between computed static Raman spectra and experimental SERS spectra makes it possible to determine stable geometries of the analyte-silver cluster complexes and to characterize the adsorption modes. The findings presented here provide a framework for designing analytical developments based on SERS for simultaneous detection of phosphonated molecules, including pesticides such as glyphosate, creating practical opportunities in key areas such as environmental and water resource in situ monitoring.

Consecutive feedback-driven constitutional dynamic networks.

Cellular transformations are driven by environmentally triggered complex dynamic networks, which include signal-triggered feedback processes, cascaded reactions, and switchable transformations. We apply the structural and functional information encoded in the sequences of nucleic acids to construct signal-triggered constitutional dynamic networks (CDNs) that mimic the functions of natural networks. Using predesigned hairpin structures as triggers, the network generates functional strands, which stabilize one or the other of the constituents of the network, leading to feedback-driven reconfiguration and time-dependent equilibration of the networks. Using structurally designed hairpins, positive-feedback or negative-feedback mechanisms operated by the CDNs are demonstrated. With two predesigned hairpins, the coupled consecutive operations of negative/positive- or positive/positive- feedback cascades are accomplished. The time-dependent composition changes of the networks are well reproduced by chemical kinetics simulations that provide predictive behaviors of the network, under variable auxiliary conditions. Beyond mimicking natural network properties and functions by means of the synthetic nucleic-acid-based CDNs, the systems introduce versatile perspectives for the design of amplified sensors (sensing of miRNA-376a) and the development of logic gate circuits.

Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses.

Electric fields can tailor molecular potential energy surfaces by interaction with the electronic state-dependent molecular dipole moment. Recent developments in optics have enabled the creation of ultrashort few-cycle optical pulses with precise control of the carrier envelope phase (CEP) that determines the offset of the maxima in the field and the pulse envelope. This opens news ways of controlling ultrafast molecular dynamics by exploiting the CEP. In this work, we show that the photoabsorption efficiency of oriented H2CSO (sulfine) can be controlled by tuning the CEP. We further show that this control emanates from a resonance condition related to Stark shifting of the electronic energy levels.

Intercommunication of DNA-Based Constitutional Dynamic Networks.

Intercommunication between dynamic chemical networks plays a major role in cellular transformations. Inspired by nature, we introduce the intercommunication between two constitutional dynamic networks, CDNs, "S" and "T" composed, each, of four equilibrated supramolecular constituents AA', AB', BA', and BB', and of CC', CD', DC', and DD', respectively. Each of the constituents is conjugated to a Mg2+-ion-dependent DNAzyme unit that acts as a reporter element for the concentration of the respective constituent via the catalyzed cleavage of the fluorophore/quencher-functionalized substrate associated with the respective DNAzyme reporter. Also, constituents BB' (in CDN "S") and CC' (in CDN "T") include Mg2+-ion-dependent DNAzymes acting as activator units for generating triggering signals between the networks. Subjecting CDNs "S" and "T" to the catalytically cleavable hairpin trigger Hdd' or Haa', respectively, yields input strands that intercommunicate the CDNs by affecting the time-dependent re-equilibration of the constituents of the counter CDN without affecting the dynamic equilibrium of the constituents of the CDN that generates the triggering strands. Treatment of CDNs "S" and "T" with hairpins Hdd' and Haa' (or Hba'), respectively, stimulates autonomous positive/positive or positive/negative feedback to the programmed time-dependent up-regulation or down-regulation of the equilibrated constituents in the two CDNs.