High-Harmonic Generation Spectroscopy of Gas-Phase Bromoform.

High-Harmonic Generation (HHG) spectra of randomly aligned bromoform (CHBr3) 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.

Peeking into the Femtosecond Hot-Carrier Dynamics Reveals Unexpected Mechanisms in Plasmonic Photocatalysis.

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.

Role of Inner Molecular Orbitals in High-Harmonic Generation Spectra of Aligned Uracil.

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 × 1014 W/cm2 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.

Deep phenotyping of the neuroimaging and skeletal features in KBG syndrome: a study of 53 patients and review of the literature.

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.

Time Evolution of Plasmonic Features in Pentagonal Ag Clusters.

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, A1) size-dependent or the high-energy (around 4 eV, E1) size-independent peak. TCMs plots on the analyzed clusters, Ag25+ and Ag43+ show off-diagonal peaks consistent with a plasmonic response when a longitudinal pulse resonant at A1 frequency is applied, and dominant diagonal spots, typical of a molecular transition, when a transverse E1 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.

Prenatal Clinical Findings in RASA1-Related Capillary Malformation-Arteriovenous Malformation Syndrome.

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.

Exceptional response to lurbinectedin and irinotecan in BRCA-mutated platinum-resistant ovarian cancer patient: a case report.

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 BRCA1-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.

Time-dependentab initioapproaches for high-harmonic generation spectroscopy.

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 anab initioelectronic-structure approach. In this review we have collected recent advances in modelling HHG by means ofab initiotime-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.

Circularly Polarized Plasmons in Chiral Gold Nanowires via Quantum-Mechanical Design.

Time-dependent density functional theory (TDDFT) simulations are conducted on a series of chiral gold nanowires to explore whether an enhancement of circular dichroism at the plasmon resonance is possible and identify its quantum-mechanical origin. We find that in linear two-dimensional chiral nanowires the dichroic response is suppressed by destructive interference of nearly degenerate components with opposite signs, pointing to this phenomenon as a common and likely origin of the difficulty encountered so far in achieving a plasmonic CD response in experiment and suggesting nevertheless that these opposite components could be "decoupled" by using multiwall arrangements. In contrast, we predict a giant dichroic response for nanowires with three-dimensional helical coiling. We rationalize this finding via an electronic structure analysis of longitudinal and transversal plasmonic excitations and their coupling into chiral components, and we propose a simple formula for the chiral response as a function of structural parameters (nanowire length and coiling number).

Role of exchange and correlation in high-harmonic generation spectra of H2, N2, and CO2: Real-time time-dependent electronic-structure approaches.

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 H2, N2, and CO2 molecules? We compare HHG spectra for H2, N2, and CO2 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.

Probing the molecular frame of uracil and thymine with high-harmonic generation spectroscopy.

In this work, we present the computed high-harmonic generation (HHG) spectra of uracil and thymine molecules, by means of the real-time time-dependent formulation of Gaussian-based configuration interaction with single excitations (RT-TD-CIS). According to the experimental work [Hutchison et al., Comparison of high-order harmonic generation in uracil and thymine ablation plumes, Phys. Chem. Chem. Phys., 2013, 15, 12308], a pulse wavelength of 780 nm has been used, together with an intensity of 1014 W cm-2 and a pulse duration of 23 optical cycles. In order to examine the effect of pulse polarisation, rotationally averaged (to mimic the gas-phase sample) and single-polarisations have been computed for both molecules. Our results show that the HHG signal for both molecules possibly originates from different ionisation channels, involving HOMO, HOMO-1, HOMO-2 and HOMO-3 orbitals, which lie within 4 eV. We characterize the HHG spectrum of thymine, supporting the idea that the absence of the thymine signal in the original work does not depend on the single-molecule behaviour. Present results for uracil are consistent with the experimental data. Moreover, we have observed that states below and above the chosen ionisation threshold provide different contributions to the HHG spectrum in averaged and single-polarisation calculations.

Plasmonic Circular Dichroism in Chiral Gold Nanowire Dimers.

We report a computational study at the time-dependent density functional theory (TDDFT) level of the chiro-optical spectra of chiral gold nanowires coupled in dimers. Our goal is to explore whether it is possible to overcome destructive interference in single nanowires that damp chiral response in these systems and to achieve intense plasmonic circular dichroism (CD) through a coupling between the nanostructures. We predict a huge enhancement of circular dichroism at the plasmon resonance when two chiral nanowires are intimately coupled in an achiral relative arrangement. Such an effect is even more pronounced when two chiral nanowires are coupled in a chiral relative arrangement. Individual component maps of rotator strength, partial contributions according to the magnetic dipole component, and induced densities allow us to fully rationalize these findings, thus opening the way to the field of plasmonic CD and its rational design.

Investigating ultrafast two-pulse experiments on single DNQDI fluorophores: a stochastic quantum approach.

Ultrafast two-pulse experiments on single molecules are invaluable tools to investigate the microscopic dynamics of a fluorophore. The first pulse generates electronic or vibronic coherence and the second pulse probes the time-evolution of the coherence. A protocol that is able to simulate ultrafast experiments on single molecules is applied in this study. It is based on a coupled quantum-mechanical description of the fluorophore and real-time dynamics of the system vibronic wave packet interacting with an electric field, described by means of the stochastic Schrödinger equation within the Markovian limit. This approach is applied to the DNQDI fluorophore, previously investigated experimentally [D. Brinks et al., Nature, 2010, 465, 905-908]. We find this to be in good agreement with the experimental outcomes and provide microscopic and atomistic interpretation.

TurboRVB: A many-body toolkit for ab initio electronic simulations by quantum Monte Carlo.

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.

Role of coherence in the plasmonic control of molecular absorption.

The interpretation of nanoplasmonic effects on molecular properties, such as metal-enhanced absorption or fluorescence, typically assumes a fully coherent picture (in the quantum-mechanical sense) of the phenomena. Yet, there may be conditions where the coherent picture breaks down, and the decoherence effect should be accounted for. Using a state-of-the-art multiscale model approach able to include environment-induced dephasing, here we show that metal nanoparticle effects on the light absorption by a nearby molecule is strongly affected (even qualitatively, i.e., suppression vs enhancement) by molecular electronic decoherence. The present work shows that decoherence can be thought of as a further design element of molecular nanoplasmonic systems.

Optimal Basis Set for Electron Dynamics in Strong Laser Fields: The case of Molecular Ion H2.

A clear understanding of the mechanisms that control the electron dynamics in a strong laser field is still a challenge that requires interpretation by advanced theory. Development of accurate theoretical and computational methods, able to provide a precise treatment of the fundamental processes generated in the strong field regime, is therefore crucial. A central aspect is the choice of the basis for the wave function expansion. Accuracy in describing multiphoton processes is strictly related to the intrinsic properties of the basis, such as numerical convergence, computational cost, and representation of the continuum. By explicitly solving the 1D and 3D time-dependent Schrödinger equation for H2+ in the presence of an intense electric field, we explore the numerical performance of using a real-space grid, a B-spline basis, and a Gaussian basis (improved by optimal Gaussian functions for the continuum). We analyze the performance of the three bases for high-harmonic generation and above-threshold ionization for H2+. In particular, for high-harmonic generation, the capability of the basis to reproduce the two-center interference and the hyper-Raman phenomena is investigated.

Probing quantum coherence in ultrafast molecular processes: An ab initio approach to open quantum systems.

Revealing possible long-living coherence in ultrafast processes allows detecting genuine quantum mechanical effects in molecules. To investigate such effects from a quantum chemistry perspective, we have developed a method for simulating the time evolution of molecular systems based on ab initio calculations, which includes relaxation and environment-induced dephasing of the molecular wave function whose rates are external parameters. The proposed approach combines a quantum chemistry description of the molecular target with a real-time propagation scheme within the time-dependent stochastic Schrödinger equation. Moreover, it allows a quantitative characterization of the state and dynamics coherence through the l1-norm of coherence and the linear entropy, respectively. To test the approach, we have simulated femtosecond pulse-shaping ultrafast spectroscopy of terrylenediimide, a well-studied fluorophore in single-molecule spectroscopy. Our approach is able to reproduce the experimental findings [R. Hildner et al., Nat. Phys. 7, 172 (2011)], confirming the usefulness of the approach and the correctness of the implementation.

Theoretical S1 ← S0 Absorption Energies of the Anionic Forms of Oxyluciferin by Variational Monte Carlo and Many-Body Green's Function Theory.

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 S1 ← S0 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 S1 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.

Ab initio lifetime correction to scattering states for time-dependent electronic-structure calculations with incomplete basis sets.

We propose a method for obtaining effective lifetimes of scattering electronic states for avoiding the artificial confinement of the wave function due to the use of incomplete basis sets in time-dependent electronic-structure calculations of atoms and molecules. In this method, using a fitting procedure, the lifetimes are extracted from the spatial asymptotic decay of the approximate scattering wave functions obtained with a given basis set. The method is based on a rigorous analysis of the complex-energy solutions of the Schrödinger equation. It gives lifetimes adapted to any given basis set without using any empirical parameters. The method can be considered as an ab initio version of the heuristic lifetime model of Klinkusch et al. [J. Chem. Phys. 131, 114304 (2009)]. The method is validated on H and He atoms using Gaussian-type basis sets for the calculation of high-harmonic-generation spectra.

Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II.

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.