37 research outputs found
Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory
No full textWe present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime (LR-TDDFT) to a set of different wave-function-based methods for excited states, namely perturbed coupled cluster (CC2), algebraic diagrammatic construction method to second order (ADC(2)), and perturbed configuration interaction (CIS(D)). 5BU has been used to investigate DNA base-amino acid interactions. In particular, it served as a model of protein-DNA photoinduced cross-linking. While LR-TDDFT is computationally the most efficient first-principles approach for static and dynamic simulations of this bichromophoric system, its accuracy is difficult to assess due to the presence of excited states with charge transfer character. In this work, the performance of different exchange correlation functionals is compared against accurate benchmarks obtained either from high level wave-function-based methods or directly from experimental absorption spectra. Our investigation shows that accurate results for the excitation energies can be obtained using the hybrid meta-GGA functional M06. In view of dynamical studies of the relaxation of 5BU after photoexcitation, we also show that the PBE functional, while failing in the Franck-Condon region, provides qualitatively good results for the characterisation of a possible photocyclization path.LCB
Assessing Nonadiabatic Dynamics Methods in Long Timescales
No full textIn this study, we employ the multiconfiguration time-dependent Hartree (MCTDH) and its multi-layer variants (ML-MCTDH), ab initio multiple spawning (AIMS), and fewest-switches surface hopping (FSSH) methodologies to simulate the excited-state dynamics of a weakly-coupled multi-dimensional (10 dimensional) Spin-Boson model Hamiltonian designed for a long timescale decay behavior. The pre-print of the article can be found at https://chemrxiv.org/engage/chemrxiv/article-details/66f68454cec5d6c142647b0a MUKHERJEE S, Lassmann Y, Mattos RS, Demoulin B, Curchod BFE, Barbatti M. Assessing Nonadiabatic Dynamics Methods in Long Timescales. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-j7xxl The dataset contains MCTDH.tar.bz2 - 10 sets of text files for MCTDH simulations ML-MCTDH.tar.vz2 - 10 sets of text files for ML-MCTDH simulations DC-FSSH.tar.bz2 - HDF5 output files for 2000 independent decoherence-corrected FSSH trajectories and a Python script for Wigner Sampling initial conditions CSS-AIMS.tar.gz - output text files for 44 independent cannibalistic stochastic selection approach of AIMS trajectorie
Exploring the Influence of Approximations for Simulating Valence Excited X-ray Spectra
No full textFirst-principles simulations of excited-state X-ray spectra are becoming increasingly important to interpret the wealth of electronic and geometric information contained within femtosecond X-ray absorption spectra recorded at X-ray Free Electron Lasers (X-FELs). However, because the transition dipole matrix elements must be calculated between two excited states (i.e., the valence excited state and the final core excited state arising from the initial valence excited state) of very different energies, this can be challenging and time-consuming to compute. Herein using two molecules, protonated formaldimine and cyclobutanone, we assess the ability of n-electron valence-state perturbation theory (NEVPT2), equation-of-motion coupled-cluster theory (EOM-CCSD), linear-response time-dependent density functional theory (LR-TDDFT) and the maximum overlap method (MOM) to describe excited state X-ray spectra. Our study focuses in particular on the behavior of these methods away from the Franck−Condon geometry and in the vicinity of important topological features of excited-state potential energy surfaces, namely, conical intersections. We demonstrate that the primary feature of excited-state X-ray spectra is associated with the core electron filling the hole created by the initial valence excitation, a process that all of the methods can capture. Higher energy states are generally weaker, but importantly much more sensitive to the nature of the reference electronic wave function. As molecular structures evolve away from the Franck−Condon geometry, changes in the spectral shape closely follow the underlying valence excitation, highlighting the importance of accurately describing the initial valence excitation to simulate the excited-state X-ray absorption spectra
Partial Density of States Representation for Accurate Deep Neural Network Predictions of X-ray Spectra
No full textThe performance of a Machine Learning (ML) algorithm for chemistry is highly contingent upon the architect’s choice of input representation. This work introduces the partial density of states (p-DOS) descriptor: a novel, quantum-inspired structural representation which encodes relevant electronic information for machine learning models seeking to simulate X-ray spectroscopy. p-DOS uses a minimal basis set in conjunction with a guess (non-optimised) electronic configuration to extract and then discretise the density of states (DOS) of the absorbing atom to form the input vector. We demonstrate that while the electronically-focused p-DOS performs well in isolation, optimal performance is achieved when supplemented with nuclear structural information imparted via a geometric representation. p-DOS provides a description of the key electronic properties of a system which is not only concise and computationally efficient, but also independent of molecular size or choice of basis set. It can be rapidly generated, facilitating its application with large training sets. Its performance is demonstrated using a wide variety of examples at the sulphur K-edge, including the prediction of ultrafast X-ray spectroscopic signal associated with photoexcited 2(5H)-thiophenone. These results highlight the potential for ML models developed using p-DOS to contribute to the interpretation and prediction of experimental results e.g. in operando measurements of batteries and/or catalysts and femtosecond time-resolved studies, especially those made possible by emergent cutting-edge technologies, especially X-ray free electron lasers.</em
Technical education and the London county council 1918-1939. A study in course innovation and development
No full textThis thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Our thesis is concerned with the process of course innovation and Development in technical education within the area of the London County Council During the period 1918-39. Although essential, an historical study, the Thesis is intended to be of value in a consideration of future development in Technical education, and in particular in the study of the relationship between Curriculum management and manpower planning. The first part of our thesis describes the institutional structure of the principal sectors of technical education in London and outlines the Type of courses that were available and their general progress during the Interwar years. The second part of our thesis seeks to analyse the background to course innovation and to assess why certain courses were successful and why others were comparative failures. Since the topic is potentially so vast, our thesis has been limited to an identification of major factors, rather than a detailed consideration of each one. Our analysis shows the process of course innovation and development in technical education to have been a highly complex interaction of forces in which the other aspects of the educational structure, including administrative as well as teach1ng institutions, played a vital role. Emphasis has been given to the influence of senior administrative officers within the local I education authority framework. Special mention has been made of the work of the Board of Education and of the limitations of the Board in tailing to establish definite guidelines for course development in technical education. Important factors outside the educational structure have also been considered, including the attitudes of parents and business management to formal technical training
The brighter-fatter effect in the JWST MIRI Si:As IBC detectors I. Observations, impact on science, and modeling
No full textContext. The Mid-Infrared Instrument (MIRI) on board the James Webb Space Telescope (JWST) uses three Si:As impurity band conduction (IBC) detector arrays. The output voltage level of each MIRI detector pixel is digitally recorded by sampling up the ramp. For uniform or low-contrast illumination, the pixel ramps become nonlinear in a predictable way, but in areas of high contrast, the nonlinearity curve becomes much more complex. The origin of the effect is poorly understood and currently not calibrated out of the data. Aims. We provide observational evidence of the brighter-fatter effect (BFE) in MIRI conventional and high-contrast coronagraphic imaging, low-resolution spectroscopy, and medium-resolution spectroscopy data, and we investigate the physical mechanism that gives rise to the effect on the MIRI detector pixel raw voltage integration ramps. Methods. We used public data from the JWST/MIRI commissioning and Cycle 1 phase. We also developed a numerical electrostatic model of the MIRI detectors using a modified version of the public Poisson_CCD code. Results. We find that the physical mechanism behind the BFE manifesting in MIRI data is fundamentally different to that of chargecoupled devices and photodiode arrays such as the Hawaii-XRG near-infrared detectors used by the NIRISS, NIRCam, and NIRSpec instruments on board JWST. Observationally, the BFE makes the JWST MIRI data yield 10-25% larger point sources and spectral line profiles as a function of the relative level of de-biasing of neighboring detector pixels. This broadening impacts the MIRI absolute flux calibration, time-series observations of faint companions, and point spread function modeling and subtraction. We also find that the intra-pixel 2D profile of the shrinking Si:As IBC detector depletion region directly impacts the accuracy of the pixel ramp nonlinearity calibration model.Planetary Exploratio
Local Control Theory in Trajectory Surface Hopping Dynamics Applied to the Excited‐State Proton Transfer of 4‐Hydroxyacridine
No full textThe application of local control theory combined with nonadiabatic ab initio molecular dynamics to study the photoinduced intramolecular proton transfer reaction in 4-hydroxyacridine was investigated. All calculations were performed within the framework of linear-response time-dependent density functional theory. The computed pulses revealed important information about the underlying excited-state nuclear dynamics highlighting the involvement of collective vibrational modes that would normally be neglected in a study performed on model systems constrained to a subset of the full configuration space. This study emphasizes the strengths of local control theory for the design of pulses that can trigger chemical reactions associated with the population of a given molecular excited state. In addition, analysis of the generated pulses can help to shed new light on the photophysics and photochemistry of complex molecular systems
Derivation of spin-orbit couplings in collinear linear-response TDDFT: a rigorous formulation
No full textUsing an approach based upon a set of auxiliary many-electron wavefunctions we present a rigorous derivation of spin-orbit coupling (SOC) within the framework of linear-response time-dependent density functional theory (LR-TDDFT). Our method is based on a perturbative correction of the non-relativistic collinear TDDFT equations using a Breit-Pauli spin-orbit Hamiltonian. The derivation, which is performed within both the Casida and Sternheimer formulations of LR-TDDFT, is valid for any basis set. The requirement of spin noncollinearity for the treatment of spin-flip transitions is also discussed and a possible alternative solution for the description of these transitions in the collinear case is also proposed. Our results are validated by computing the SOC matrix elements between singlet and triplet states of two molecules, formaldehyde and acetone. In both cases, we find excellent agreement with benchmark calculations performed with a high level correlated wavefunction method
Capturing the interplay between spin-orbit coupling and non-Condon effects on the photoabsorption spectra of Ru and Os dyes
No full text\ua9 2019 The Royal Society of Chemistry.In this work, we investigate the factors influencing the shape of the low-energy tail of the absorption spectrum of a homoleptic biscyclometalated ruthenium complex with terdentate ligands [T. W. Rees et al., Inorg. Chem., 2017, 56, 9903] by combining an advanced theoretical strategy and the synthesis of an analogous osmium complex. The theoretical protocol merges relativistic linear-response time-dependent density functional theory and the nuclear ensemble approach, permitting to shed light on the influence of spin-orbit coupling and non-Condon effects on the theoretical absorption spectra of these rather large metal complexes
How a toxic pollutant avoids photodegradation: Relaxation pathways of UV-excited 2,4-dinitrophenol in aqueous solution
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