Search

In the present work, we apply recently developed real-time descriptors to study the time evolution of plasmonic features of pentagonal Ag clusters. The method is based on the propagation of the time-dependent Schrödinger equation within a singly excited TDDFT ansatz. We use transition contribution maps (TCMs) and induced density to characterize the optical longitudinal and transverse response of such clusters, when interacting with pulses resonant with the low-energy (around 2–3 eV, A 1 ) size-dependent or the high-energy (around 4 eV, E 1 ) size-independent peak. TCMs plots on the analyzed clusters, Ag 25 + and Ag 43 + show off-diagonal peaks consistent with a plasmonic response when a longitudinal pulse resonant at A 1 frequency is applied, and dominant diagonal spots, typical of a molecular transition, when a transverse E 1 pulse is employed. Induced densities confirm this behavior, with a dipole-like charge distribution in the first case. The optical features show a time delay with respect to the evolution of the external pulse, consistent with those found in the literature for real-time TDDFT calculations on metal clusters. [ABSTRACT FROM AUTHOR]

High-harmonic generation (HHG) spectroscopy was investigated from laser ablation plasmas of uracil targets in the experimental work of Hutchinson et al., [ Phys. Chem. Chem. Phys. Comparison of high-order harmonic generation in uracil and thymine ablation plumes , 2013, 15 , 12308] and of Lopez-Quintas et al. , [ Appl. Surf. Sci., Characterization of laser-induced plasmas of nucleobases: Uracil and thymine , 2014, 302 , 299]. Inspired by these works we computed HHG spectra of uracil cation fragments by means of real-time time-dependent configuration interaction with single excitations (RT-TD-CIS) and continuum-optimal Gaussian basis sets. We calculated the rotationally-averaged HHG spectra of different cation fragments analysing the relation between HHG, geometry of the fragments (linear/nonlinear) and electron dynamics (bound and continuum energy states). Moreover, to simulate the complexity of a sample containing fragments upon ablation, we calculated weighted-rotationally-averaged HHG spectra where the contribution of each fragment is included through weights assigned accordingly to the experimental mass spectra. [ABSTRACT FROM AUTHOR]

Broad-spectrum genetic tests often lead to the identification of variants of uncertain significance (VUS), a major issue in modern clinical genetics. A fair proportion of VUS may alter the splicing processes, but their interpretation is challenging. This study aimed at providing a classification approach for VUS potentially-affecting splicing by integrating transcript analysis from peripheral blood mRNA into routine diagnostics. VUS in DICER1, MSH2, MLH1, DYNC1H1, RPS6KA3, and SCN9A, found in patients with phenotypes compatible with the related syndromes, altered splicing, leading to their re-classification as Pathogenic/Likely Pathogenic. This had a significant clinical impact for different diseases, from hereditary tumor predisposition to neurological and congenital syndromic disorders. Transcript analysis is valuable in VUS clinical evaluation, and its incorporation into routine diagnostic workflows facilitates timely and accurate clinical decision-making., (© 2024 The Author(s). Clinical Genetics published by John Wiley & Sons Ltd.)

We propose a real-time time-dependent ab initio approach within a configuration-interaction-singles ansatz to decompose the high-harmonic generation (HHG) signal of molecules in terms of individual molecular-orbital (MO) contributions. Calculations have been performed by propagating the time-dependent Schrödinger equation with complex energies, in order to account for ionization of the system, and by using tailored Gaussian basis sets for high-energy and continuum states. We have studied the strong-field electron dynamics and the HHG spectra in aligned CO2 and H2O molecules. Contribution from MOs in the strong-field dynamics depends on the interplay between the MO ionization energy and the coupling between the MO and the laser-pulse symmetries. Such contributions characterize different portions of the HHG spectrum, indicating that the orbital decomposition encodes nontrivial information on the modulation of the strong-field dynamics. Our results correctly reproduce the MO contributions to HHG for CO2 as described in the literature experimental and theoretical data and lead to an original analysis of the role of the highest occupied molecular orbitals HOMO, HOMO-1, and HOMO-2 of H2O according to the polarization direction of the laser pulse., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

We present a multiscale method coupling the theory of open quantum systems with real-time ab initio treatment of electronic structure to study hot-carrier dynamics in photoexcited plasmonic systems. We combine the Markovian Stochastic Schrödinger equation with an ab initio GW coupled to the Bethe-Salpeter (BSE) equation description of the electronic degrees of freedom, interacting with a metallic nanoparticle modeled classically according to the polarizable continuum model. We apply this methodology to study the effect of relaxation (T1) and pure dephasing (T2) times on the hot-carrier dynamics in a system composed of a quantum portion described at GW/BSE level, i.e., a CHO fragment adsorbed on a vertex of a rhodium nanocube, and of the rest of the nanocube, treated classically, when irradiated with a 2.7 eV light pulse, inspired by the experimental results on plasmon-driven CO2 photoreduction. A net hole injection from rhodium to CHO is observed, with and without the classical portion of the nanocube. The nanocube effect is to enhance the generated charge population by two orders of magnitude. The nonradiative decay, via a relaxation time T1 based on the energy-gap law, produces a rapid decrease of the charge population. Results with T2 only show that a charge injection retarded with respect to the pulse, which is present in the coherent dynamics, disappears when coherence is erased., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Following changes in chirality can give access to relevant information on the function or reactivity of molecular systems. Time-resolved circular dichroism (TRCD) spectroscopy proves to be a valid tool to achieve this goal. Depending on the class of molecules, different temporal ranges, spanning from seconds to femtoseconds, need to be investigated to observe such chiroptical changes. Therefore, over the years, several approaches have been adopted to cover the timescale of interest, especially based on pump-probe schemes. Moreover, various theoretical approaches have been proposed to simulate and explain TRCD spectra, including linear and non-linear response methods as well as non-adiabatic molecular dynamics. In this review, an overview on both experimental and theoretical advances in the TRCD field is provided, together with selected applications. A discussion on future theoretical developments for TRCD is also given.

High-Harmonic Generation (HHG) spectra of randomly aligned bromoform (CHBr 3 ) molecules have been experimentally measured and theoretically simulated at various laser pulse intensities. From the experiments, we obtained a significant number of harmonics that goes beyond the cutoff limit predicted by the three-step model (3SM) with ionization from HOMO. To interpret the experiment, we resorted to real-time time-dependent configuration interaction with single excitations. We found that electronic bound states provide an appreciable contribution to the harmonics. More in detail, we analyzed the electron dynamics by decomposing the HHG signal in terms of single molecular-orbital contributions, to explain the appearance of harmonics around 20-30 eV beyond the expected cutoff due to HOMO. HHG spectra can be therefore explained by considering the contribution at high energy of HOMO-6 and HOMO-9, thus indicating a complex multiple-orbital strong-field dynamics. However, even though the presence of the bromoform cation should be not enough to produce such a signal, we could not exclude a priori that the origin of harmonics in the H29-H45 to be due to the cation, which has more energetic ionization channels.

Plasmonic-driven photocatalysis may lead to reaction selectivity that cannot be otherwise achieved. A fundamental role is played by hot carriers, i.e., electrons and holes generated upon plasmonic decay within the metal nanostructure interacting with molecular species. Understanding the elusive microscopic mechanism behind such selectivity is a key step in the rational design of hot-carrier reactions. To accomplish that, we present state-of-the-art multiscale simulations, going beyond density functional theory, of hot-carrier injections for the rate-determining step of a photocatalytic reaction. We focus on carbon dioxide reduction, for which it was experimentally shown that the presence of a rhodium nanocube under illumination leads to the selective production of methane against carbon monoxide. We show that selectivity is due to a (predominantly) direct hole injection from rhodium to the reaction intermediate CHO. Unexpectedly, such an injection does not promote the selective reaction path by favoring proper bond breaking but rather by promoting bonding of the proper molecular fragment to the surface.

Background: KBG syndrome is caused by haploinsufficiency of ANKRD11 and is characterised by macrodontia of upper central incisors, distinctive facial features, short stature, skeletal anomalies, developmental delay, brain malformations and seizures. The central nervous system (CNS) and skeletal features remain poorly defined., Methods: CNS and/or skeletal imaging were collected from molecularly confirmed individuals with KBG syndrome through an international network. We evaluated the original imaging and compared our results with data in the literature., Results: We identified 53 individuals, 44 with CNS and 40 with skeletal imaging. Common CNS findings included incomplete hippocampal inversion and posterior fossa malformations; these were significantly more common than previously reported (63.4% and 65.9% vs 1.1% and 24.7%, respectively). Additional features included patulous internal auditory canal, never described before in KBG syndrome, and the recurrence of ventriculomegaly, encephalic cysts, empty sella and low-lying conus medullaris. We found no correlation between these structural anomalies and epilepsy or intellectual disability. Prevalent skeletal findings comprised abnormalities of the spine including scoliosis, coccygeal anomalies and cervical ribs. Hand X-rays revealed frequent abnormalities of carpal bone morphology and maturation, including a greater delay in ossification compared with metacarpal/phalanx bones., Conclusion: This cohort enabled us to describe the prevalence of very heterogeneous neuroradiological and skeletal anomalies in KBG syndrome. Knowledge of the spectrum of such anomalies will aid diagnostic accuracy, improve patient care and provide a reference for future research on the effects of ANKRD11 variants in skeletal and brain development., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

In this work, we decompose the high-harmonic generation (HHG) signal of aligned gas-phase uracil into single molecular-orbital (MO) contributions. We compute HHG spectra for a pulse linearly polarized perpendicular to the molecular plane, with an intensity of 0.6 and 0.85 × 10 14 W/cm 2 and a wavelength of 800 nm. We use the real-time time-dependent Configuration Interaction with singles method, coupled to a Gaussian-based representation of the time-dependent wavefunction. The strong-field dynamics is affected by the energy of the ionization/recombination channels and by the coupling between the orbital symmetry and laser polarization. In the configuration studied here, we expect that π-type MOs favorably couple with the incoming pulse and play a substantial role in generating the HHG spectrum. Indeed, we show that HOMO, HOMO - 1, and HOMO - 4, which all are π-like, determine the intensity of harmonic peaks at different energies, while HOMO - 2 and HOMO - 3 provide a smaller contribution. It is worth mentioning that HOMO - 4 produces a stronger signal than that from HOMO - 1, even though the corresponding ionization energy, in an one-electron picture, is around 2.5 eV larger and more than 4 eV larger than the HOMO one.

Pathogenic variants in RASA1 are typically associated with a clinical condition called "capillary malformation-arteriovenous malformation" (CM-AVM) syndrome, an autosomal dominant genetic disease characterized by a broad phenotypic variability, even within families. In CM-AVM syndrome, multifocal capillary and arteriovenous malformations are mainly localized in the central nervous system, spine and skin. Although CM-AVM syndrome has been widely described in the literature, only 21 cases with prenatal onset of clinical features have been reported thus far. Here, we report four pediatric cases of molecularly confirmed CM-AVM syndrome which manifested during the prenatal period. Polyhydramnios, non-immune hydrops fetalis and chylothorax are only a few possible aspects of this condition, but a correct interpretation of these prenatal signs is essential due to the possible fatal consequences of unrecognized encephalic and thoracoabdominal deep vascular malformations in newborns and in family members carrying the same RASA1 variant.

Lurbinectedin is responsible for DNA recognition and binding, producing double-strand DNA (dsDNA) breaks thus resulting in apoptosis. Sensitivity to lurbinectedin is linked to the nucleotide excision repair (NER) system. Furthermore, irinotecan, a topoisomerase I inhibitor, provokes dsDNA breaks that could be reinforced abrogating the NER system using lurbinectedin. BRCA -mutated patients, already treated with platinum-derived drugs, who suffered DNA damage, cannot repair the breaks due to lurbinectedin interaction, whereas irinotecan provokes a dsDNA break that promotes synthetic lethality. This article describes an exceptional response to lurbinectedin alone followed by the association with irinotecan in a BRCA -mutated platinum-resistant ovarian cancer patient. A 44-year-old BRCA 1-mutated ovarian cancer patient was treated in sixth line with lurbinectedin and irinotecan with a time to further progression (TTFP) equal to 8 months. In our case, the association with irinotecan overcame the resistance to lurbinectedin alone. In conclusion, lurbinectedin and irinotecan demonstrated a promising response in platinum-resistant patients. However, further studies should be conducted to validate our findings and future trials will be important to further define the clinical utility of lurbinectedin., Competing Interests: Conflict of interest statement: The authors declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article: LC: honoraria: AstraZeneca, MSD, Pfizer; Consulting or Advisory Role: Pfizer, Novartis, GSK, Clovis. No other potential conflicts of interest were reported., (© The Author(s), 2022.)

High-harmonic generation (HHG) is a nonlinear physical process used for the production of ultrashort pulses in XUV region, which are then used for investigating ultrafast phenomena in time-resolved spectroscopies. Moreover, HHG signal itself encodes information on electronic structure and dynamics of the target, possibly coupled to the nuclear degrees of freedom. Investigating HHG signal leads to HHG spectroscopy, which is applied to atoms, molecules, solids and recently also to liquids. Analysing the number of generated harmonics, their intensity and shape gives a detailed insight of, e.g., ionisation and recombination channels occurring in the strong-field dynamics. A number of valuable theoretical models has been developed over the years to explain and interpret HHG features, with the three-step model being the most known one. Originally, these models neglect the complexity of the propagating electronic wavefunction, by only using an approximated formulation of ground and continuum states. Many effects unravelled by HHG spectroscopy are instead due to electron correlation effects, quantum interference, and Rydberg-state contributions, which are all properly captured by an ab initio electronic-structure approach. In this review we have collected recent advances in modelling HHG by means of ab initio time-dependent approaches relying on the propagation of the time-dependent Schrödinger equation (or derived equations) in presence of a very intense electromagnetic field. We limit ourselves to gas-phase atomic and molecular targets, and to solids. We focus on the various levels of theory employed for describing the electronic structure of the target, coupled with strong-field dynamics and ionisation approaches, and on the basis used to represent electronic states. Selected applications and perspectives for future developments are also given., (© 2021 IOP Publishing Ltd.)

This study arises from the attempt to answer the following question: how different descriptions of electronic exchange and correlation affect the high-harmonic generation (HHG) spectroscopy of H 2 , N 2 , and CO 2 molecules? We compare HHG spectra for H 2 , N 2 , and CO 2 with different ab initio electronic structure methods: real-time time-dependent configuration interaction and real-time time-dependent density functional theory (RT-TDDFT) using truncated basis sets composed of correlated wave functions expanded on Gaussian basis sets. In the framework of RT-TDDFT, we employ Perdew-Burke-Ernzerhof (PBE) and long-range corrected Perdew-Burke-Ernzerhof (LC-ωPBE) functionals. We study HHG spectroscopy by disentangling the effect of electronic exchange and correlation. We first analyze the electronic exchange alone, and in the case of RT-TDDFT with LC-ωPBE, we use ω = 0.3 and ω = 0.4 to tune the percentage of long-range Hartree-Fock exchange and short-range exchange PBE. Then, we added the correlation as described by the PBE functional. All the methods give very similar HHG spectra, and they seem not to be particularly sensitive to the different description of exchange and correlation or to the correct asymptotic behavior of the Coulomb potential. Despite this general trend, some differences are found in the region connecting the cutoff and the background. Here, the harmonics can be resolved with different accuracy depending on the theoretical schemes used. We believe that the investigation of the molecular continuum and its coupling with strong fields merits further theoretical investigations in the near future.

TurboRVB is a computational package for ab initio Quantum Monte Carlo (QMC) simulations of both molecular and bulk electronic systems. The code implements two types of well established QMC algorithms: Variational Monte Carlo (VMC) and diffusion Monte Carlo in its robust and efficient lattice regularized variant. A key feature of the code is the possibility of using strongly correlated many-body wave functions (WFs), capable of describing several materials with very high accuracy, even when standard mean-field approaches [e.g., density functional theory (DFT)] fail. The electronic WF is obtained by applying a Jastrow factor, which takes into account dynamical correlations, to the most general mean-field ground state, written either as an antisymmetrized geminal power with spin-singlet pairing or as a Pfaffian, including both singlet and triplet correlations. This WF can be viewed as an efficient implementation of the so-called resonating valence bond (RVB) Ansatz, first proposed by Pauling and Anderson in quantum chemistry [L. Pauling, The Nature of the Chemical Bond (Cornell University Press, 1960)] and condensed matter physics [P.W. Anderson, Mat. Res. Bull 8, 153 (1973)], respectively. The RVB Ansatz implemented in TurboRVB has a large variational freedom, including the Jastrow correlated Slater determinant as its simplest, but nontrivial case. Moreover, it has the remarkable advantage of remaining with an affordable computational cost, proportional to the one spent for the evaluation of a single Slater determinant. Therefore, its application to large systems is computationally feasible. The WF is expanded in a localized basis set. Several basis set functions are implemented, such as Gaussian, Slater, and mixed types, with no restriction on the choice of their contraction. The code implements the adjoint algorithmic differentiation that enables a very efficient evaluation of energy derivatives, comprising the ionic forces. Thus, one can perform structural optimizations and molecular dynamics in the canonical NVT ensemble at the VMC level. For the electronic part, a full WF optimization (Jastrow and antisymmetric parts together) is made possible, thanks to state-of-the-art stochastic algorithms for energy minimization. In the optimization procedure, the first guess can be obtained at the mean-field level by a built-in DFT driver. The code has been efficiently parallelized by using a hybrid MPI-OpenMP protocol, which is also an ideal environment for exploiting the computational power of modern Graphics Processing Unit accelerators.

Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunlight is absorbed by the chlorophylls of the antenna and subsequently conveyed to the reaction center of Photosystem II through resonant energy transfer mechanisms. In the special pair of chlorophylls of the reaction center the charge separation occurs, eventually leading to the oxidation of water molecules into protons, electrons and molecular oxygen. The adsorption properties of the antenna chlorophylls are ad hoc modulated by the protein environment to guarantee fast energy transfer and minimize side and back reactions. At the same time these properties are influenced by the molecular fluctuations occurring at physiological temperature. In the present work, combining classical molecular dynamics simulations with the Charge Density Coupling method, we estimated the impact of the thermal fluctuations on the site energy shift of the chlorophylls embedded in the Photosystem II complex. Our results show how the effect of the molecular fluctuations is not homogeneous throughout the complex, although the symmetry of the homodimer is maintained. Many peripheral chromophores undergo fluctuations larger then 10kJ/mol around the average values. Possible physiological roles of such fluctuations are discussed., (Copyright © 2017 Elsevier B.V. All rights reserved.)

The structures of three negatively charged forms (anionic keto-1 and enol-1 and dianionic enol-2) of oxyluciferin (OxyLuc), which are the most probable emitters responsible for the firefly bioluminescence, have been fully relaxed at the variational Monte Carlo (VMC) level. Absorption energies of the S 1 ← S 0 vertical transition have been computed using different levels of theory, such as TDDFT, CC2, and many-body Green's function theory (MBGFT). The use of MBGFT, by means of the Bethe-Salpeter (BS) formalism, on VMC structures provides results in excellent agreement with the value (2.26(8) eV) obtained by action spectroscopy experiments for the keto-1 form (2.32 eV). To unravel the role of the quality of the optimized ground-state geometry, BS excitation energies have also been computed on CASSCF geometries, inducing a non-negligible blue shift (0.08 and 0.07 eV for keto-1 and enol-1 forms, respectively) with respect to the VMC ones. Structural effects have been analyzed in terms of over- or undercorrelation along the conjugated bonds of OxyLuc by using different methods for the ground-state optimization. The relative stability of the S 1 state for the keto-1 and enol-1 forms depends on the method chosen for the excited-state calculation, thus representing a fundamental caveat for any theoretical study on these systems. Finally, Kohn-Sham HOMO and LUMO orbitals of enol-2 are (nearly) bound only when the dianion is embedded into a solvent (water and toluene in the present work); excited-state calculations are therefore meaningful only in the presence of a dielectric medium which localizes the electronic density. The combination of VMC for the ground-state geometry and BS formalism for the absorption spectra clearly outperforms standard TDDFT and quantum chemistry approaches.

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.

The accurate determination of the geometrical details of the dark state of 11- cis retinal in rhodopsin represents a fundamental step for the rationalization of the protein role in the optical spectral tuning in the vision mechanism. We have calculated geometries of the full retinal protonated Schiff base chromophore in the gas phase and in the protein environment using the correlated variational Monte Carlo method. The bond length alternation of the conjugated carbon chain of the chromophore in the gas phase shows a significant reduction when moving from the β -ionone ring to the nitrogen, whereas, as expected, the protein environment reduces the electronic conjugation. The proposed dark state structure is fully compatible with solid-state NMR data reported by Carravetta et al. [ J. Am. Chem. Soc . 2004 , 126 , 3948-3953]. TDDFT/B3LYP calculations on such geometries show a blue opsin shift of 0.28 and 0.24 eV induced by the protein for S 1 and S 2 states, consistently with literature spectroscopic data. The effect of the geometrical distortion alone is a red shift of 0.21 and 0.16 eV with respect to the optimized gas phase chromophore. Our results open new perspectives for the study of the properties of chromophores in their biological environment using correlated methods.

Variational and diffusion Monte Carlo (VMC and DMC) calculations are presented for anionic electrolytes solvated in (4)He. The electrolytes have the general structure X(-)(He)(N), with X=F, Cl, Br and I, and N varying up to 40 (41 for I(-)). The overall interaction potential is obtained from accurate ab initio data for the two-body components and then using the sum-of-potentials approximation. Our computational scheme is a robust procedure, giving us accurate trial wavefunctions that can be used to perform high-quality DMC calculations. The results indicate very marked delocalization and permanence of the liquid-like quantum features of the solvent adatoms surrounding the anionic impurities. This finding stands in contrast to the more structured, solid-like behavior of the quantum solutions with alkali metal cations embedded in He nanodroplets. While other negatively charged species such as H(-) have shown an overall repulsive interaction with He, the present calculations clearly indicate that the halogen anions remain solvated within liquid-like solvent "bubbles" of species-dependent size.

Nothing is more false than the image of Dante as an isolated genius standing out against his epoch. On the contrary he belongs to a very characteristic generation of italian intellectuals: laymen, often active in more than one domain, practicing abundantly poetic expression, engaged in political action, these scholar-citizens share equally a strong historical conscience. Their inventivity is manifested in philosophy, in medecine and in law, as well as in literary expression. Aside from these endogenous factors, a key to this phenomenon is linked to the active reception of the naturalistic knowledge elaborated in Paris, which is read in Italy outside of the control of theologians. The parallel journeys of a dozen uncommon personalities show the necessity of enlarging the habitual frames of medieval intellectual history.