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The outcomes and timescales of molecular nonadiabatic dynamics are decisively impacted by the quantum coherences generated at localized molecular regions. In time-resolved X-ray diffraction imaging, these coherences create distinct signatures via inelastic photon scattering, but they are buried under much stronger background elastic features. Here, we exploit the rich dynamical information encoded in the inelastic patterns, which we reveal by frequency-dispersed covariance ultrafast powder X-ray diffraction of stochastic X-ray free-electron laser pulses. This is demonstrated for the photoisomerization of azobenzene involving the passage through a conical intersection, where the nuclear wave packet branches and explores different quantum pathways. Snapshots of the coherence dynamics are obtained at high frequency shifts, not accessible with conventional diffraction measurements. These provide access to the timing and to the confined spatial distribution of the valence electrons directly involved in the conical intersection passage. This study can be extended to full three-dimensional imaging of conical intersections with ultrafast X-ray and electron diffraction.
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X-ray diffraction is routinely used for structure determination of stationary molecular samples. Modern X-ray photon sources, e.g., from free-electron lasers, enable us to add temporal resolution to these scattering events, thereby providing a movie of atomic motions. We simulate and decipher the various contributions to the X-ray diffraction pattern for the femtosecond isomerization of azobenzene, a textbook photochemical process. A wealth of information is encoded besides real-time monitoring of the molecular charge density for the cis to trans isomerization. In particular, vibronic coherences emerge at the conical intersection, contributing to the total diffraction signal by mixed elastic and inelastic photon scattering. They cause distinct phase modulations in momentum space, which directly reflect the real-space phase modulation of the electronic transition density during the nonadiabatic passage. To overcome the masking by the intense elastic scattering contributions from the electronic populations in the total diffraction signal, we discuss how this information can be retrieved, e.g., by employing very hard X-rays to record large scattering momentum transfers.
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The fate of virtually all photochemical reactions is determined by conical intersections. These are energetically degenerate regions of molecular potential energy surfaces that strongly couple electronic states, thereby enabling fast relaxation channels. Their direct spectroscopic detection relies on weak features that are often buried beneath stronger, less interesting contributions. For azobenzene photoisomerization, a textbook photochemical reaction, we demonstrate how a resonant infrared field can be employed during the conical intersection passage to significantly enhance its coherence signatures in time-resolved X-ray diffraction while leaving the product yield intact. This transition-state amplification holds promise to bring signals of conical intersections above the detection threshold.
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We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Calculations at two levels of electronic structure theory, time-dependent density functional theory (with NWChem) and RASSCF/RASPT2 (with OpenMolcas) are presented and compared where possible. The iSPECTRON program is available online at https://github.com/ispectrongit/iSPECTRON/ and distributed open source under the terms of the Educational Community License version 2.0 (ECL 2.0).
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Core excitations on different atoms are highly localized and therefore decoupled. By placing molecules in an x-ray cavity the core transitions become coupled via the exchange of cavity photons and form delocalized hybrid light-matter excitations known as core polaritons. We demonstrate these effects for the two inequivalent carbon atoms in 1,1-difluoroethylene. Polariton signatures in the x-ray absorption, two-photon absorption, and multidimensional four-wave mixing signals are predicted.
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Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment-protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics.
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Complexos de Proteínas Captadores de Luz/química , Modelos Químicos , Ácidos Nucleicos/química , Teoria Quântica , TermodinâmicaRESUMO
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.
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Peptídeos/química , Dicroísmo Circular , Conformação Proteica , Espectrofotometria UltravioletaRESUMO
MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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X-ray spectroscopy is gaining a growing interest in the scientific community, as it represents a versatile and powerful experimental toolbox for probing the dynamics of both core and valence electronic excitations, nuclear motions and material structure, with element and site specificity. Among the various X-ray based techniques, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, which investigates the energy and probability of resonant core-to-valence transitions, has started to be applied to organic molecules: a recent UV-pump X-ray probe time-resolved NEXAFS experiment [Wolf et al., Nat. Commun., 2017, 8, 1] has shown the capability of the technique to provide information about the ultrafast internal conversion between the bright ππ* and the dark nπ* electronic states of the nucleobase thymine. In the present contribution we introduce an accurate theoretical approach for the simulation of NEXAFS spectra of organic molecules, employing azobenzene as a test case. The electronic structure calculations, which provide both energy levels and transition probabilities of core-to-valence excitations, were here performed with a high level multiconfigurational method, the restricted active space self consistent field (RASSCF/RASPT2). GS- and nπ*-NEXAFS spectra were obtained on the top of key molecular geometries (as the optimized cis, trans and conical intersection(s) structures) as well as along the fundamental isomerization coordinates (namely, symmetric and asymmetric bendings of the phenyl rings, and torsion around the central dihedral). We eventually characterize and explain the origin of the simulated signals, highlighting the specific signatures that make it possible to follow the excited state evolution from the nπ* Franck-Condon point, towards the conical intersection(s).
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In this discussion we present a methodology to describe spectral lineshape from first principles, providing insight into the solvent-solute molecular interactions in terms of static and dynamic disorder and how these shape the signals recorded experimentally in linear and nonlinear optical spectroscopies, including two-dimensional electronic spectroscopy (2DES). Two different strategies for simulating the lineshape are compared: both rely on the same evaluation of the coupling between the electronic states and the intra-molecular vibrations, while they differ in describing the influence exerted by the diverse water configurations attained along a molecular dynamics (MD) simulation. The first method accounts for such water arrangements as first order perturbations on the adenine energies computed for a single reference (gas phase) quantum calculation. The second method requires computation of the manifold of excited states explicitly at each simulation snapshot, employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. Both approaches are applied to a large number of states of the adenine singlet excited manifold (chosen because of its biological role), and compared with available experimental data. They give comparable results but the first approach is two orders of magnitude faster. We show how the various contributions (static/dynamic disorder, intra-/inter-molecular interactions) sum up to build the total broadening observed in experiments.
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Linear and nonlinear X-ray spectroscopy hold the promise to provide a complementary tool to the available ample body of terahertz to UV spectroscopic techniques, disclosing information about the electronic structure and the dynamics of a large variety of systems, spanning from transition metals to organic molecules. While experimental free electron laser facilities continue to develop, theory may take the lead in modeling and inspiring new cutting edge experiments, paving the way to their future use. As an example, the not-yet-available two-dimensional coherent X-ray spectroscopy (2DCXS), conceptually similar to 2D-NMR, is expected to provide a wealth of information about molecular structure and dynamics with an unprecedented level of detail. In the present contribution, we focus on the simulation of linear and non-linear (2DCXS) spectra of the ESCA molecule. The molecule has four inequivalent carbon K-edges and has been widely used as a benchmark for photoelectron spectroscopy. Two theoretical approaches for the computation of the system manifold of states, namely, TDDFT and RASSCF/RASPT2, are compared, and the possible signals that may appear in a 2DCXS experiment and their origin are surveyed.
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By comparing two-dimensional electronic spectroscopy (2DES) and Pump-Probe (PP) measurements on xanthorhodopsin (XR) and reduced-xanthorhodopsin (RXR) complexes, the ultrafast carotenoid-to-retinal energy transfer pathway is revealed, at very early times, by an excess of signal amplitude at the associated cross-peak and by the carotenoid bleaching reduction due to its ground state recovery. The combination of the measured 2DES and PP spectroscopic data with theoretical modelling allows a clear identification of the main experimental signals and a comprehensive interpretation of their origin and dynamics. The remarkable velocity of the energy transfer, despite the non-negligible energy separation between the two chromophores, and the analysis of the underlying transport mechanism, highlight the role played by the ground state carotenoid vibrations in assisting the process.
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Nonlinear electronic spectroscopies represent one of the most powerful techniques to study complex multichromophoric architectures. For these systems, in fact, linear spectra are too congested to be used to disentangle the many coupled vibroelectronic processes that are activated. By using a 2D approach, instead, a clear picture can be achieved, but only when the recorded spectra are combined with a proper interpretative model. So far, this has been almost always achieved through parametrized exciton Hamiltonians that necessarily introduce biases and/or arbitrary assumptions. In this study, a first-principles approach is presented that combines accurate quantum chemical descriptions with state-of-the-art models for the environment through the use of atomistic and polarizable embeddings. Slow and fast bath dynamics, along with exciton transport between the pigments, are included. This approach is applied to the 2DES spectroscopy of the Light-Harvesting 2 (LH2) complex of purple bacteria. Simulations are extended over the entire visible-near-infrared spectral region to cover both carotenoid and bacteriochlorophyll signals. Our results provide an accurate description of excitonic properties and relaxation pathways, and give an unprecedented insight into the interpretation of the spectral signatures of the measured 2D signals.
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INTRODUCTION: The identification of early-stage colorectal cancers (CRC) and the resection of pre-cancerous neoplastic lesions through colonoscopy allows to decrease both CRC incidence and mortality. However, colonoscopy miss rates up to 26% for adenomas and 9% for advanced adenomas have been reported. In recent years, artificial intelligence (AI) systems have been emerging as easy-to-use tools, potentially lowering the risk of missing lesions. AREAS COVERED: This review paper focuses on GI Genius device (Medtronic Co. Minneapolis, MN, U.S.A.) a computer-assisted tool designed to assist endoscopists during standard white-light colonoscopies in detecting mucosal lesions. EXPERT OPINION: Randomized controlled trials (RCTs) suggest that GI Genius is a safe and effective tool for improving adenoma detection, especially in CRC screening and surveillance colonoscopies. However, its impact seems to be less significant among experienced endoscopists and in real-world clinical scenarios compared to the controlled conditions of RCTs. Furthermore, it appears that GI Genius mainly enhances the detection of non-advanced, small polyps, but does not significantly impact the identification of advanced and difficult-to-detect adenoma. When using GI Genius, no complications were documented. Only a small number of studies reported an increased in withdrawal time or the removal of non-neoplastic lesions.
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Neoplasias Colorretais , Humanos , Neoplasias Colorretais/diagnóstico , Colonoscopia/métodos , Adenoma/diagnóstico , Adenoma/diagnóstico por imagem , Inteligência ArtificialRESUMO
Expressions for linear and nonlinear spectroscopy simulation in the X-ray window in which the time evolution of a photoexcited molecular system is treated via quantum dynamics are derived. By leveraging on the peculiar properties of core-excited/ionized states, first- and third-order response functions are recast in the limit of time-scale separation between the extremely short core-state lifetime and the (comparably longer) electronic-state transfer and nuclear vibrational motion. This work is a natural extension of Segatta et al. (J. Chem. Theory Comput. 2023, 19, 2075-2091), in which some of the present authors coupled MCTDH quantum dynamics to spectroscopy simulation at different levels of sophistication. Full quantum dynamics and approximate expressions are compared by simulating X-ray transient absorption spectroscopy at the carbon K-edge in the pyrene molecule.
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We report the development of a novel diagnostic tool, named wave function overlap tool (WFOT), designed to evaluate the overlap between wave functions computed at single-reference [i.e., time-dependent density functional theory or configuration interaction singles (CIS)] and multireference (i.e., CASSCF/CASPT2) electronic structure levels of theory. It relies on truncating the single- and multireference WFs to CIS-like expansions spanning the same configurational space and maximizing the molecular orbital overlap by means of a unitary transformation. To demonstrate the functionality of the tool, we calculate the transient spectrum of acetylacetone by evaluating excited state absorption signals with multireference quality on top of single-reference on-the-fly dynamics simulations. Semiautomatic spectra generation is facilitated by interfacing the tool with the COBRAMM package, which also allows one to use WFOT with several quantum chemistry codes such as Gaussian, NWChem, and OpenMolcas. Other exciting possibilities for the utilization of the code beyond the simulation of transient absorption spectroscopy are eventually discussed.
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We present an accurate and efficient approach to computing the linear and nonlinear optical spectroscopy of a closed quantum system subject to impulsive interactions with an incident electromagnetic field. It incorporates the effect of ultrafast nonadiabatic dynamics by means of explicit numerical propagation of the nuclear wave packet. The fundamental expressions for the evaluation of first- and higher-order response functions are recast in a general form that can be used with any quantum dynamics code capable of computing the overlap of nuclear wave packets evolving in different states. Here we present the evaluation of these expressions with the multiconfiguration time-dependent Hartree (MCTDH) method. Application is made to pyrene, excited to its lowest bright excited state S2 which exhibits a sub-100-fs nonadiabatic decay to a dark state S1. The system is described by a linear vibronic coupling Hamiltonian, parametrized with multiconfiguration electronic structure methods. We show that the ultrafast nonadiabatic dynamics can have a remarkable effect on the spectral line shapes that goes beyond simple lifetime broadening. Furthermore, a widely employed approximate expression based on the time scale separation of dephasing and population relaxation is recast in the same theoretical framework. Application to pyrene shows the range of validity of such approximations.
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Multireference methods are known for their ability to accurately treat states of very different nature in many molecular systems, facilitating high-quality simulations of a large variety of spectroscopic techniques. Here, we couple the multiconfigurational restricted active space self-consistent field RASSCF/RASPT2 method (of the CASSCF/CASPT2 methods family) to the displaced harmonic oscillator (DHO) model, to simulate soft X-ray spectroscopy. We applied such an RASSCF/RASPT2+DHO approach at the K-edges of various second-row elements for a set of small organic molecules that have been recently investigated at other levels of theory. X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) are simulated with a sub-eV accuracy and a correct description of the spectral line shapes. The method is extremely sensitive to the observed spectral shifts on a series of differently fluorinated ethylene systems, provides spectral fingerprints to distinguish between stable conformers of the glycine molecule, and accurately captures the vibrationally resolved carbon K-edge spectrum of formaldehyde. Differences with other theoretical methods are demonstrated, which show the advantages of employing a multireference/multiconfigurational approach. A protocol to systematically increase the number of core-excited states considered while maintaining a contained computational cost is presented. Insight is eventually provided for the effects caused by removing core-electrons from a given atom in terms of bond rearrangement and influence on the resulting spectral shapes within a unitary orbital-based framework for both XPS and XANES spectra.