Multidimensional X-Ray Spectroscopy of Valence and Core Excitations in Cysteine
TL;DR: The coupling between valence- and core-excited states can be visualized in three-dimensional plots, revealing the origin of the polarizability that controls the simpler pump-probe SXRS signals.
Abstract: Several nonlinear spectroscopy experiments which employ broadband x-ray pulses to probe the coupling between localized core and delocalized valence excitation are simulated for the amino acid cysteine at the K-edges of oxygen and nitrogen and the K and L-edges of sulfur. We focus on two dimensional (2D) and 3D signals generated by two- and three-pulse stimulated x-ray Raman spectroscopy (SXRS) with frequency-dispersed probe. We show how the four-pulse x-ray signals $\boldsymbol{k}_\mathrm{I}=-\boldsymbol{k}_1+\boldsymbol{k}_2+\boldsymbol{k}_3$ and $\boldsymbol{k}_\mathrm{II}=\boldsymbol{k}_1-\boldsymbol{k}_2+\boldsymbol{k}_3$ can give new 3D insight into the SXRS signals. The coupling between valence- and core-excited states can be visualized in three dimensional plots, revealing the origin of the polarizability that controls the simpler pump-probe SXRS signals.
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TL;DR: The off-resonant scattering of a broadband X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states is calculated using a quantum electrodynamic framework and can guide future experimental studies on the structures of nano-particles and proteins.
Abstract: Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broadband X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins.
32 citations
TL;DR: In this article, a review of the state-of-the-art multi-pulse experimental schemes for 2D IR spectroscopy has been presented, some of which allow one to simultaneously examine anharmonic vibrational interactions and frequency-frequency correlations among vibrational chromophores having very different vibrational frequencies, particularly in a broadband fashion.
Abstract: Over the last decade, ultrafast two-dimensional infrared (2D IR) spectroscopy has been greatly advanced in a variety of aspects and is becoming a more exciting vibrational tool for understanding the structures and dynamics of condensed-phase equilibrium and non-equilibrium molecular systems, as well as surface-immobilised monolayers or adsorbates. A number of novel multi-pulse experimental schemes have been reported, some of them allow one to simultaneously examine anharmonic vibrational interactions and frequency–frequency correlations among vibrational chromophores having very different vibrational frequencies, particularly in a broadband fashion, providing potentially intrinsic spectroscopic probes for local, regional, and global molecular structures and dynamics; and some of them allow one to access more vibrational levels of a given set of anharmonic oscillators, enabling a better characterisation of their anharmonic potentials and factors influencing them. In this review, we first introduce ...
31 citations
TL;DR: This chapter surveys the basic description of nonlinear X-ray spectroscopy signals and the electronic structure protocols which may be used for their simulation.
Abstract: Measuring the nonlinear response of electrons and nuclei to attosecond broadband X-ray radiation has become possible by newly developed free electron lasers and high harmonic generation light sources The design and interpretation of these novel experiments poses considerable computational challenges In this chapter we survey the basic description of nonlinear X-ray spectroscopy signals and the electronic structure protocols which may be used for their simulation
29 citations
TL;DR: The capabilities of 2DRR spectroscopy are discussed in the context of recent applications to the photodissociation reactions of triiodide and myoglobin and great potential for the future of the technique is suggested.
Abstract: Two-dimensional resonance Raman (2DRR) spectroscopy has been developed for studies of photochemical reaction mechanisms and structural heterogeneity in complex systems. The 2DRR method can leverage electronic resonance enhancement to selectively probe chromophores embedded in complex environments (e.g., a cofactor in a protein). In addition, correlations between the two dimensions of the 2DRR spectrum reveal information that is not available in traditional Raman techniques. For example, distributions of reactant and product geometries can be correlated in systems that undergo chemical reactions on the femtosecond time scale. Structural heterogeneity in an ensemble may also be reflected in the 2D spectroscopic line shapes of both reactive and non-reactive systems. In this perspective article, these capabilities of 2DRR spectroscopy are discussed in the context of recent applications to the photodissociation reactions of triiodide and myoglobin. We also address key differences between the signal generation ...
25 citations
TL;DR: This work addresses impulsive stimulated Raman spectroscopy (ISRS), a powerful technique able to coherently stimulate and record Raman-active modes using broadband pulses with novel control knobs to selectively enhance desired vibrational features and distinguish spectral components arising from different excited states.
Abstract: Photophysical and photochemical processes are often dominated by molecular vibrations in various electronic states. Dissecting the corresponding, often overlapping, spectroscopic signals from different electronic states is a challenge hampering their interpretation. Here we address impulsive stimulated Raman spectroscopy (ISRS), a powerful technique able to coherently stimulate and record Raman-active modes using broadband pulses. Using a quantum-mechanical treatment of the ISRS process, we show the mode-specific way the various spectral components of the broadband probe contribute to the signal generated at a given wavelength. We experimentally demonstrate how to manipulate the signal by varying the probe chirp and the phase-matching across the sample, thereby affecting the relative phase between the various contributions to the signal. These novel control knobs allow us to selectively enhance desired vibrational features and distinguish spectral components arising from different excited states.
24 citations
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TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
Abstract: Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact‐exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange‐correlation functional containing local‐spin‐density, gradient, and exact‐exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first‐ and second‐row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
87,732 citations
TL;DR: In this article, the unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio using DFT, MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set.
Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg
17,871 citations
TL;DR: In this article, a new hybrid exchange-correlation functional named CAM-B3LYP is proposed, which combines the hybrid qualities of B3LYP and the long-range correction presented by Tawada et al.
10,882 citations
Book•
01 Jan 1987
TL;DR: In this paper, the dynamics of nuclear spin systems were studied by two-dimensional exchange spectroscopy and nuclear magnetic resonance imaging (NEMI) imaging, and two different correlation methods based on coherence transfer were proposed.
Abstract: List of notation Introduction The dynamics of nuclear spin systems Manipulation of nuclear spin Hamiltonians One-dimensional Fourier spectroscopy Multiple-quantum transitions Two-dimensional Fourier spectroscopy Two-dimensional separation of interactions Two-dimensional correlation methods based on coherence transfer Dynamic processes studied by two-dimensional exchange spectroscopy Nuclear magnetic resonance imaging References Index.
4,977 citations
TL;DR: An overview of NWChem is provided focusing primarily on the core theoretical modules provided by the code and their parallel performance, as well as Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures.
4,666 citations