A fully dynamical description of time-resolved resonant inelastic X-ray scattering of pyrazine.

Recent advancements in ultrashort and intense X-ray sources have enabled the utilisation of resonant inelastic X-ray scattering (RIXS) as a probing technique for monitoring photoinduced dynamics in molecular systems. To account for dynamic phenomena like non-adiabatic transitions across the relevant electronic state manifold, a time-dependent framework is crucial. Here, we introduce a fully time-dependent approach for calculating transient RIXS spectra using wavepacket dynamics simulations, alongside an explicit treatment of the X-ray probe pulse that surpasses Kramers-Heisenberg-Dirac constraints. Our analysis of pyrazine at the nitrogen K-edge underscores the importance of considering nuclear motion effects in all electronic states involved in the transient RIXS process. As a result, we propose a numerically exact approach to computationally support and predict cutting-edge time-resolved RIXS experiments.

Rational Design of Phe-BODIPY Amino Acids as Fluorogenic Building Blocks for Peptide-Based Detection of Urinary Tract Candida Infections.

Fungal infections caused by Candida species are among the most prevalent in hospitalized patients. However, current methods for the detection of Candida fungal cells in clinical samples rely on time-consuming assays that hamper rapid and reliable diagnosis. Herein, we describe the rational development of new Phe-BODIPY amino acids as small fluorogenic building blocks and their application to generate fluorescent antimicrobial peptides for rapid labelling of Candida cells in urine. We have used computational methods to analyse the fluorogenic behaviour of BODIPY-substituted aromatic amino acids and performed bioactivity and confocal microscopy experiments in different strains to confirm the utility and versatility of peptides incorporating Phe-BODIPYs. Finally, we have designed a simple and sensitive fluorescence-based assay for the detection of Candida albicans in human urine samples.

A Rare Dirhamnosyl Flavonoid and Other Radical-Scavenging Metabolites from Cynophalla mollis (Kunth) J.†Presl and Colicodendron scabridum (Kunt) Seem. (Capparaceae) of Ecuador.

The phytochemistry of Cynophalla mollis (Kunth) J. Presl and Colicodendron scabridum (Kunth), both belonging to the family Capparaceae, were investigated in this study for the first time. Lupeol, betulin, lutein, stachydrine and quercetin-3,4'-di-O-rhamnoside were isolated from C. mollis, whereas C. scabridum afforded lupeol, lutein, stachydrine, ß-sitosterol, stigmasterol, betonicine and narcissoside. All these compounds were purified by preparative liquid chromatography, in both open column and instrumental (MPLC) separation systems. Preparative TLC was also applied. They were all identified by 1 H- and 13 C-NMR experiments. The complete structure of the very rare flavonoid quercetin-3,4'-di-O-rhamnoside was fully elucidated through DEPT-135, COSY, HMQC and HMBC experiments, together with UV/VIS and FT-IR spectrophotometry. Complete NMR data for quercetin-3,4'-di-O-rhamnoside in deuterated methanol were presented here for the first time. All the extracts did not exert antioxidant activity at the maximum tested dose of 1 mg/mL. Three out of the nine isolated compounds exerted a good spectrum of antioxidant capacity, being narcissoside the most active against ABTS radicals, with SC50 =12.43 µM. It was followed by lutein and quercetin-3,4'-di-O-rhamnoside, with 40.92 µM and 46.10 µM, respectively.

Modifications to cytoskeleton-associated proteins in dendritic spines underlie the adaptive plasticity involved in long term reference memory.

Spatial learning and memory enables individuals to orientate themselves in an external environment. Synaptic stimulation of dendritic spines on hippocampal place cells underlies adaptive cognitive performance, inducing plastic changes such as spinogenesis, pruning and structural interconversion. Such plastic changes are driven by complex molecular machinery that relies on several actin cytoskeleton-associated proteins (ACAP's), these interacting with actin filaments in the postsynaptic density to guide the conformational changes to spines in accordance with the synaptic information they receive. However, the specific dynamics of the plastic changes in spines driven by ACAP's are poorly understood. Adult rats exhibit efficient allocentric reference memory 30 days after training in a spatial learning paradigm in the Morris water maze. A Golgi study revealed this behavior to be associated with a reduction in both spine density and in mushroom spines, as well as a concomitant increase in thin spines. These changes were accompanied by the overexpression of mRNA encoding ß-actin, Spinophilin and Cortactin, whilst the expression of Profilin, α-actinin, Drebrin, Synaptopodin and Myosin decreased. By contrast, no changes were evident in Cofilin, Gelsolin and Arp2/3 mRNA. From this analysis, it appears that neither spinogenesis nor new mushroom spines are necessary for long-term spatial information retrieval, while thin spines could be potentiated to retrieve pre-learned spatial information. Further studies that focus on the signaling pathways and their related molecules may shed further light on the molecular dynamics of the plastic changes to dendritic spines that underlie cognitive performance, both under normal and pathological conditions.

Regularizing the MCTDH equations of motion through an optimal choice on-the-fly (i.e., spawning) of unoccupied single-particle functions.

The multi-configuration time-dependent Hartree method is a general algorithm to solve the time-dependent Schrödinger equation, in which the wavefunction is expanded in a direct product of self-adapting time-dependent Single-Particle Functions (SPFs) that are propagated in time according to the Dirac-Frenkel variational principle. In the current version of this approach, the size of the SPF basis is fixed at the outset so that singularities in the working equations resulting from unoccupied functions have to be removed by a regularization procedure. Here, an alternative protocol is presented, in which we gradually increase the number of unoccupied SPFs on-the-fly (i.e., spawning) and optimize their shape by variationally minimizing the error made by the finite size of the basis. An initial estimate for the respective new expansion coefficients is also computed, thus avoiding the need to regularize the equations of motion. The advantages of employing the new algorithm are tested and discussed in some illustrative examples.

Comparison of mortality and viral load in rainbow trout (Oncorhynchus mykiss) infected with infectious pancreatic necrosis virus (IPNV) genogroups 1 and 5.

Infectious pancreatic necrosis virus (IPNV) is the aetiological agent of a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into eight genogroups, of which two are present in Chile, genogroups 1 and 5. Here, we compare the mortality rate caused by isolates from both genogroups in rainbow trout (Oncorhynchus mykiss) fry to determine if there is an association between host susceptibility and phylogenetic characterization of IPNV. Fish were challenged by immersion with one of four isolates (two for each genogroup), and mortality curves were assessed after 30 days. Viral load was measured in all mortalities and in live fish sampled at 1, 7 and 20 days post-infection. Although mortality was low throughout the challenge, differences were found between fish infected with different isolates. Both isolates from genogroup 1 caused greater cumulative mortalities than either of the isolates from genogroup 5. When combined, the overall mortality rate of fish challenged with genogroup 1 isolates was significantly higher than those infected with genogroup 5. However, viral load was lower on trout infected with genogroup 1 isolates. These results suggest that rainbow trout are more susceptible to IPNV isolates from genogroup 1 than genogroup 5.

Tg.rasH2 Mouse Model for Assessing Carcinogenic Potential of Pharmaceuticals: Industry Survey of Current Practices.

The Tg.rasH2 mouse was developed as an alternative model to the traditional 2-year mouse bioassay for pharmaceutical carcinogenicity testing. This model has found extensive use in support of pharmaceutical drug development over the last few decades. It has the potential to improve quality and timeliness, reduce animal usage, and in some instances allow expedient decision-making regarding the human carcinogenicity potential of a drug candidate. Despite the increased use of the Tg.rasH2 model, there has been no systematic survey of current practices in the design, interpretation of results from the bioassay, and global health authority perspectives. Therefore, the aim of this work was to poll the pharmaceutical industry on study design practices used in the dose range finding and definitive 6-month studies and on results relative to the ongoing negotiations to revise The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use S1 Guidance. Twenty-two member companies of International Consortium for Innovation and Quality in Pharmaceutical Development DruSafe Leadership Group participated in the survey, sharing experiences from studies conducted with 55 test compounds between 2010 and 2018. The survey results provide very useful insights into study design and interpretation. Importantly, the results identified several key opportunities for reducing animal use and increasing the value of testing for potential human carcinogenicity using this model. Recommended changes to study designs that would reduce animal usage include eliminating the requirement to include positive control groups in every study, use of nontransgenic wild-type littermates in the dose range finding study, and use of microsampling to reduce or eliminate satellite groups for toxicokinetics.

Accidental degeneracy in the spiropyran radical cation: charge transfer between two orthogonal rings inducing ultra-efficient reactivity.

Photochromism of the spiropyran radical cation to the corresponding merocyanine form is investigated by a combination of electrochemical oxidation, UV/vis absorption spectroscopy, spectroelectrochemistry and first-principles calculations (TD-DFT, CAS-SCF and CAS-PT2). First, we demonstrate that the ring-opening of mono-spiropyrans occurs upon one-electron oxidation and that it can be driven photochemically as well as thermally, with trapping of the merocyanine by protonation. Second, in order to explain this experimentally observed spectroelectrochemical behaviour we suggest a theoretical mechanism based on the reactivity of the two lowest electronic excited-states, which promotes effective electron transfer from the indoline (nitrogen-ring) to the pyran (oxygen-ring) moieties (and vice versa) through a conical intersection seam of degeneracy. Characterisation of the minimum energy conical intersection on this crossing revealed that it presents a rare diabatic trapping topology. The excited state molecule cannot escape from crossing the intersection seam due to the presence of only one degeneracy-lifting coordinate that efficiently channels into the formation of the merocyanine photoproduct, so giving rise to a "kitchen sink" funnel-like effect. Therefore, assuming rapid relaxation after vertical excitation to a higher electronic state, photoconversion cannot be avoided in the D1 electronic state, which rationalises the remarkably efficient visible light driven excited-state reactivity observed experimentally.

Quantum effects in ultrafast electron transfers within cryptochromes.

Cryptochromes and photolyases are flavoproteins that may undergo ultrafast charge separation upon electronic excitation of their flavin cofactors. Charge separation involves chains of three or four tryptophan residues depending on the protein of interest. The molecular mechanisms of these processes are not completely clear. In the present work we investigate the relevance of quantum effects like the occurrence of nuclear tunneling and of coherences upon charge transfer in Arabidopsis thaliana cryptochromes. The possible breakdown of the Condon approximation is also investigated. We have devised a simulation protocol based on the realization of molecular dynamics simulations on diabatic potential energy surfaces defined at the hybrid constrained density functional theory/molecular mechanics level. The outcomes of the simulations are analyzed through various dedicated kinetics schemes related to the Marcus theory that account for the aforementioned quantum effects. MD simulations also provide a basic material to define realistic model Hamiltonians for subsequent quantum dissipative dynamics. To carry out quantum simulations, we have implemented an algorithm based on the Hierarchical Equations of Motion. With this new tool in hand we have been able to model the electron transfer chain considering either two- or three-state models. Kinetic models and quantum simulations converge to the conclusion that quantum effects have a significant impact on the rate of charge separation. Nuclear tunneling involving atoms of the tryptophan redox cofactors as well as of the environment (protein atoms and water molecules) is significant. On the other hand non-Condon effects are negligible in most simulations. Taken together, the results of the present work provide new insights into the molecular mechanisms controlling charge separation in this family of flavoproteins.

N-confused porphyrin tautomers: lessons from density functional theory.

Using first-principle calculations, we characterize the properties of N-confused porphyrins (NCP), with a focus on the differences between the 2H and 3H tautomers. We find that NCP-3H is almost as strongly aromatic as porphyrin, and about twice as aromatic, i.e., remarkably more stable, than NCP-2H, due to the less efficient π-conjugation in the latter form. The deprotonation of the NH-group at the external side of the inverted ring of NCP-2H, adds a lone pair to the π-system, which restores a strong aromaticity, while methylation has no significant effect. Investigating the impact of solvation using a continuum model, we find quite stable solvation energies with a relative dielectric constant, εr, in the 5-40 range, for both tautomers. NCP-3H presents a slightly lower energy than its NCP-2H counterpart in all solvents. However, the energy differences between the two species are of the order of the error margin of the method, hence too small to discuss the experimentally observed stabilization of NCP-3H in dichloromethane (DCM, a poorly polar solvent) and NCP-2H in N,N-dimethylformamide (DMF, a strongly polar solvent) or to extract the population ratios between the two forms in the different solvents. Therefore, the vibronic absorption spectra are also investigated in an effort to rationalize the complex absorption profiles of these NCP derivatives. We find very distinct spectra for the 2H and 3H forms in DMF and DCM, respectively, each fairly reproducing the experiment. We also find that, in the same solvent, the two species exhibit very different signatures, which allows us to conclude that the 2H and 3H tautomers are largely dominant in DMF and DCM, respectively. Interestingly, the vibrational motions that strongly participate in the shoulder of the Soret band and the multiple maxima of the Q-bands largely differ in the two tautomers.

Electronic control of initial nuclear dynamics adjacent to a conical intersection.

Photoionization can create a nonstationary electronic state and therefore initiates coupled electron-nuclear dynamics in molecules. Using a CASSCF implementation of the Ehrenfest method, we study the nuclear dynamics following vertical ionization of toluene, starting close to the conical intersection between ground and first excited states of its cation. The results show how the initial nuclear dynamics is controlled by the nonstationary electronic state character. In particular, ionization of this system leading to an equal superposition of the two lowest energy states can initiate nuclear dynamics in an orthogonal direction in the branching space to dynamics on the ground or first excited state potential energy surfaces alone.

Characterisation of a novel Fc conjugate of macrophage colony-stimulating factor.

We have produced an Fc conjugate of colony-stimulating factor (CSF) 1 with an improved circulating half-life. CSF1-Fc retained its macrophage growth-promoting activity, and did not induce proinflammatory cytokines in vitro. Treatment with CSF1-Fc did not produce adverse effects in mice or pigs. The impact of CSF1-Fc was examined using the Csf1r-enhanced green fluorescent protein (EGFP) reporter gene in MacGreen mice. Administration of CSF1-Fc to mice drove extensive infiltration of all tissues by Csf1r-EGFP positive macrophages. The main consequence was hepatosplenomegaly, associated with proliferation of hepatocytes. Expression profiles of the liver indicated that infiltrating macrophages produced candidate mediators of hepatocyte proliferation including urokinase, tumor necrosis factor, and interleukin 6. CSF1-Fc also promoted osteoclastogenesis and produced pleiotropic effects on other organ systems, notably the testis, where CSF1-dependent macrophages have been implicated in homeostasis. However, it did not affect other putative CSF1 targets, notably intestine, where Paneth cell numbers and villus architecture were unchanged. CSF1 has therapeutic potential in regenerative medicine in multiple organs. We suggest that the CSF1-Fc conjugate retains this potential, and may permit daily delivery by injection rather than continuous infusion required for the core molecule.

Comparison of effectiveness of cefovecin, doxycycline, and amoxicillin for the treatment of experimentally induced early Lyme borreliosis in dogs.

BACKGROUND: While Koch's postulates have been fulfilled for Lyme disease; causing transient fever, anorexia and arthritis in young dogs; treatment of sero-positive dogs, especially asymptomatic animals, remains a topic of debate. To complicate this matter the currently recommended antibiotic treatments of Lyme Disease in dogs caused by Borrelia burgdorferi require daily oral administrations for 31 days or longer, which makes non-compliance a concern. Additionally, there is no approved veterinary antimicrobial for the treatment of Lyme Disease in dogs in the USA and few recommended treatments have been robustly tested. In vitro testing of cefovecin, a novel extended-spectrum cephalosporin, demonstrated inhibition of spirochete growth. A small pilot study in dogs indicated that two cefovecin injections two weeks apart would be as efficacious against B. burgdorferi sensu stricto as the recommended treatments using doxycycline or amoxicillin daily for 31 days. This hypothesis was tested in 17-18 week old Beagle dogs, experimentally infected with B. burgdorferi sensu stricto, using wild caught ticks, 75 days prior to antimicrobial administration. RESULTS: Clinical observations for lameness were performed daily but were inconclusive as this characteristic sign of Lyme Disease rarely develops in the standard laboratory models of experimentally induced infection. However, each antibiotic tested was efficacious against B. burgdorferi as measured by a rapid elimination of spirochetes from the skin and reduced levels of circulating antibodies to B. burgdorferi. In addition, significantly less cefovecin treated animals had Lyme Disease associated histopathological changes compared to untreated dogs. CONCLUSIONS: Convenia was efficacious against B. burgdorferi sensu stricto infection in dogs as determined by serological testing, PCR and histopathology results. Convenia provides an additional and effective treatment option for Lyme Disease in dogs.

Electron dynamics upon ionization: control of the timescale through chemical substitution and effect of nuclear motion.

Photoionization can generate a non-stationary electronic state, which leads to coupled electron-nuclear dynamics in molecules. In this article, we choose benzene cation as a prototype because vertical ionization of the neutral species leads to a Jahn-Teller degeneracy between ground and first excited states of the cation. Starting with equal populations of ground and first excited states, there is no electron dynamics in this case. However, if we add methyl substituents that break symmetry but do not radically alter the electronic structure, we see charge migration: oscillations in the spin density that we can correlate with particular localized electronic structures, with a period depending on the gap between the states initially populated. We have also investigated the effect of nuclear motion on electron dynamics using a complete active space self-consistent field (CASSCF) implementation of the Ehrenfest method, most previous theoretical studies of electron dynamics having been carried out with fixed nuclei. In toluene cation for instance, simulations where the nuclei are allowed to move show significant differences in the electron dynamics after 3 fs, compared to simulations with fixed nuclei.

New insights into the by-product fatigue mechanism of the photo-induced ring-opening in diarylethenes.

The photochromic properties of diarylethenes, some of the most studied class of molecular switches, are known to be controlled by non-adiabatic decay at a conical intersection seam. Nevertheless, as their fatigue-reaction mechanism - leading to non-photochromic products - is yet to be understood, we investigate the photo-chemical formation of the so-called by-product isomer using three complementary computational methods (MMVB, CASSCF and CASPT2) on three model systems of increasing complexity. We show that for the ring-opening reaction a transition state on S1(2A) involving bond breaking of the penta-ring leads to a low energy S1(2A)/S0(1A) conical intersection seam, which lies above one of the transition states leading to the by-product isomer on the ground state. Therefore, radiationless decay and subsequent side-product formation can take place explaining the photo-degradation responsible for the by-product generation in diarylethene-type molecules. The effect of dynamic electron correlation and the possible role of inter-system crossing along the penta-ring opening coordinate are discussed as well.

Time-Dependent Resonant Inelastic X-ray Scattering of Pyrazine at the Nitrogen K-Edge: A Quantum Dynamics Approach.

We calculate resonant inelastic X-ray scattering spectra of pyrazine at the nitrogen K-edge in the time domain including wavepacket dynamics in both the valence and core-excited state manifolds. Upon resonant excitation, we observe ultrafast non-adiabatic population transfer between core-excited states within the core-hole lifetime, leading to molecular symmetry distortions. Importantly, our time-domain approach inherently contains the ability to manipulate the dynamics of this process by detuning the excitation energy, which effectively shortens the scattering duration. We also explore the impact of pulsed incident X-ray radiation, which provides a foundation for state-of-the-art time-resolved experiments with coherent pulsed light sources.

Estradiol-mediated modulation of memory and of the underlying dendritic spine plasticity through the life span.

The morphophysiology of the nervous system changes and adapts in response to external environmental inputs and the experiences of individuals throughout their lives. Other changes in the organisms internal environment can also contribute to nervous system restructuring in the form of plastic changes that underlie its capacity to adapt to emerging psychophysiological conditions. These adaptive processes lead to subtle modifications of the organisms internal homeostasis which is closely related with the activity of chemical messengers, such as neurotransmitters and hormones. Hormones reach the brain through the bloodstream, where they activate specific receptors through which certain biochemical, physiological, and morphological changes take place in numerous regions. Fetal development, infancy, puberty, and adulthood are all periods of substantial hormone-mediated brain remodeling in both males and females. Adulthood, specifically, is associated with a broad range of life events, including reproductive cycles in both sexes, and pregnancy and menopause in women. Events of this kind occur concomitantly with eventual modifications in behavioral performance and, especially, in cognitive abilities like learning and memory that underlie, at least in part, plastic changes in the dendritic spines of the neuronal cells in cerebral areas involved in processing cognitive information. Estrogens form a family that consists of three molecules [17ß-estradiol (E2), estrone, estriol] which are deeply involved in regulating numerous bodily functions in different stages of the life-cycle, including the modulation of cognitive performance. This review addresses the effects of E2 on the dendritic spine-mediated synaptic organization of cognitive performance throughout the life span.

How the conical intersection seam controls chemical selectivity in the photocycloaddition of ethylene and benzene.

The photocycloaddition reaction of benzene with ethylene has been studied at the CASSCF level, including the characterization of an extended conical intersection seam. We show that the chemical selectivity is, in part, controlled by this extended conical intersection seam and that the shape of the conical intersection seam can be understood in terms of simple VB arguments. Further, the shape and energetics of the asynchronous segment of the conical intersection seam suggest that 1,2 (ortho) and 1,3 (meta) will be the preferred chemical products with similar weight. The 1,4 (para) point on the conical intersection is higher in energy and corresponds to a local maximum on the seam. VB analysis shows that the pairs of VB structures along this asynchronous seam are the same and thus the shape will be determined mainly by steric effects. Synchronous structures on the seam are higher in energy and belong to a different branch of the seam separated by a saddle point on the seam. On S1 we have documented three mechanistic pathways corresponding to transition states (with low barriers) between the reactants and the conical intersection seam: a mixed asynchronous/synchronous [1,2] ortho path, an asynchronous [1,3] meta path, and a synchronous [1,3] meta path.

Coupled electron-nuclear dynamics: charge migration and charge transfer initiated near a conical intersection.

Coupled electron-nuclear dynamics, implemented using the Ehrenfest method, has been used to study charge migration with fixed nuclei, together with charge transfer when nuclei are allowed to move. Simulations were initiated at reference geometries of neutral benzene and 2-phenylethylamine (PEA), and at geometries close to potential energy surface crossings in the cations. Cationic eigenstates, and the so-called sudden approximation, involving removal of an electron from a correlated ground-state wavefunction for the neutral species, were used as initial conditions. Charge migration without coupled nuclear motion could be observed if the Ehrenfest simulation, using the sudden approximation, was started near a conical intersection where the states were both strongly coupled and quasi-degenerate. Further, the main features associated with charge migration were still recognizable when the nuclear motion was allowed to couple. In the benzene radical cation, starting from the reference neutral geometry with the sudden approximation, one could observe sub-femtosecond charge migration with a small amplitude, which results from weak interaction with higher electronic states. However, we were able to engineer large amplitude charge migration, with a period between 10 and 100 fs, corresponding to oscillation of the electronic structure between the quinoid and anti-quinoid cationic electronic configurations, by distorting the geometry along the derivative coupling vector from the D6h Jahn-Teller crossing to lower symmetry where the states are not degenerate. When the nuclear motion becomes coupled, the period changes only slightly. In PEA, in an Ehrenfest trajectory starting from the D2 eigenstate and reference geometry, a partial charge transfer occurs after about 12 fs near the first crossing between D1, D2 (N(+)-Phenyl, N-Phenyl(+)). If the Ehrenfest propagation is started near this point, using the sudden approximation without coupled nuclear motion, one observes an oscillation of the spin density--charge migration--between the N atom and the phenyl ring with a period of 4 fs. When the nuclear motion becomes coupled, this oscillation persists in a damped form, followed by an effective charge transfer after 30 fs.

Optimal Mode Combination in the Multiconfiguration Time-Dependent Hartree Method through Multivariate Statistics: Factor Analysis and Hierarchical Clustering.

The multiconfiguration time-dependent Hartree (MCTDH) method and its multilayer extension (ML-MCTDH) are powerful algorithms for the efficient computation of nuclear quantum dynamics in high-dimensional systems. By providing time-dependent variational orbitals and an optimal choice of layered effective degrees of freedom, one is able to reduce the computational cost to an amenable number of configurations. However, choices related to selecting properly the mode grouping and tensor tree are strongly system dependent and, thus far, subjectively based on intuition and/or experience. Therefore, herein we detail a new protocol based on multivariate statistics─more specifically, factor analysis and hierarchical clustering─for a reliable and convenient guiding in the optimal design of such complex "system-of-systems" tensor-network decompositions. The advantages of employing the new algorithm and its applicability are tested on water and two floppy protonated water clusters with large amplitude motions.