Multidimensional Spectroscopy Research Articles

Homonuclear J-couplings and heteronuclear structural constraints

In magic angle spinning (MAS) experiments involving uniformly 13C,15N proteins, 13C–13C and 13C–15N dipolar recoupling experiments are now routinely used to measure direct dipole–dipole couplings that constrain distances and torsion angles and determine molecular structures. When the distances are short (<4 Å), the direct couplings dominate the evolution of the spin system, and the 13C–13C and 13C–15N J-couplings (scalar couplings) are ignored. However, for structurally interesting >4 Å distances, the dipolar and J-couplings are generally of comparable magnitude, and the variation in J must be included in order to optimize the precision of the experiment. This problem is circumvented in cases with well resolved spectra by using frequency-selective dipolar recoupling methods where the effects of J-couplings are refocused. However, for larger molecules with more spectral crowding, the requisite pulse length to achieve selectivity becomes long and leads to unacceptable sensitivity losses during the pulse or the spectral overlap precludes selective excitation. In this paper, we address this problem with two approaches aimed at facilitating higher precision internuclear distance measurements in systems that are not fully resolved. Namely, (1) we describe an approach for high precision measurements of specific J-couplings using the in-phase anti-phase (IPAP) sequence which is integrated into a non-selective dipolar recoupling technique and (2) we utilize the measured J-couplings to implement a double quantum filter experiment capable of providing the resolution necessary for frequency selective dipolar recoupling techniques without resorting to multidimensional spectroscopy. We illustrate these methods using a 7-peptide segment from the amyloidogenic Sup-35p protein, U-13C/15N-GNNQQNY, where we have measured 25 of the 27 possible one bond 13C–13C J-couplings.

Ultrafast and Coherent Dynamics in a Solvent Switchable "Pink Box" Perylene Diimide Dimer.

Perylene diimide (PDI) dimers and higher aggregates are key components in organic molecular photonics and photovoltaic devices, supporting singlet fission and symmetry breaking charge separation. Detailed understanding of their excited states is thus important. This has proven challenging because interchromophoric coupling is a strong function of dimer architecture. Recently, a macrocyclic PDI dimer was reported in which excitonic coupling could be turned on and off simply by changing the solvent. This presents a useful case where coupling is modified without synthetic changes to tune supramolecular structure. Here we present a detailed study of solvent dependent excited state dynamics in this dimer by means of coherent multidimensional spectroscopy. Spectral analysis resolves the different coupling strengths, which are consistent with solvent dependent changes in dimer conformation. The strongly coupled conformer forms an excimer within 300 fs. The low-frequency Raman active modes recovered from two-dimensional electronic spectra reveal frequencies characteristic of exciton coupling. These are assigned to modes modulating the coupling from the corresponding DFT calculations. Further analysis reveals a time dependent frequency during excimer formation. Analysis of two-dimensional "beatmaps" reveals features in the coupled dimer which are not predicted by the displaced harmonic oscillator model and are assigned to vibronic coupling.

Investigation on concentration detection of turbid solution based on hemisphere sample cell and multidimensional spectroscopy

The study developed a hemisphere sample cell and constructed a multidimensional spectroscopy acquisition system to enhance the accuracy of detecting turbid solution with scattering properties. The system simultaneously captures absorption and scattering information from the tested samples. Monte Carlo simulation was employed to model the transmission light intensity distribution data from sample cells of various shapes. It was found that the hemisphere sample cell increases the dimensionality of transmission light intensity information and enables the acquisition of more scattering-related data. Furthermore, 46 samples of intralipid-20% solution with varying concentrations were examined. Models were constructed using partial least squares (PLS) regression with one-dimensional and two-dimensional light intensity distribution data. The results indicate that the model using two-dimensional light intensity distribution data significantly outperforms the model using one-dimensional data, reducing the root mean square error by 39.96% and increasing the correlation coefficient by 0.332%. Experimental results demonstrate that the multidimensional spectroscopic modeling method employing the hemisphere sample cell can significantly enhance the accuracy and speed of detecting chemical composition concentrations in turbid solution.

Ultrafast and Coherent Dynamics in a Solvent Switchable “Pink Box” Perylene Diimide Dimer

AbstractPerylene diimide (PDI) dimers and higher aggregates are key components in organic molecular photonics and photovoltaic devices, supporting singlet fission and symmetry breaking charge separation. Detailed understanding of their excited states is thus important. This has proven challenging because interchromophoric coupling is a strong function of dimer architecture. Recently, a macrocyclic PDI dimer was reported in which excitonic coupling could be turned on and off simply by changing the solvent. This presents a useful case where coupling is modified without synthetic changes to tune supramolecular structure. Here we present a detailed study of solvent dependent excited state dynamics in this dimer by means of coherent multidimensional spectroscopy. Spectral analysis resolves the different coupling strengths, which are consistent with solvent dependent changes in dimer conformation. The strongly coupled conformer forms an excimer within 300 fs. The low‐frequency Raman active modes recovered from two‐dimensional electronic spectra reveal frequencies characteristic of exciton coupling. These are assigned to modes modulating the coupling from the corresponding DFT calculations. Further analysis reveals a time dependent frequency during excimer formation. Analysis of two‐dimensional “beatmaps” reveals features in the coupled dimer which are not predicted by the displaced harmonic oscillator model and are assigned to vibronic coupling.

Multidimensional fluorescence spectroscopy of wine using synchronous excitation/emission matrices and time-resolved fluorescence interferometric detection

Wines are complex mixtures of chemical compounds with broad and overlapping absorption and emission spectral features in the UV and visible spectral regions, making them challenging to study with conventional optical spectroscopic techniques. Multidimensional fluorescence spectroscopies correlate fluorescence spectra with other degrees of freedom, and have proven useful for studying complex molecular systems, offering a pathway for the analysis of wines utilising their inherent fluorescence. Here we employ steady-state excitation-emission matrix (EEM) and time-resolved fluorescence spectral measurements to investigate representative commercial white and red wine samples and a fluorescent ‘model’ wine base. Combining these multidimensional measurement methods provides information on the emission characteristics of the components that wines contain. This investigation illustrates the potential for multidimensional fluorescence techniques as diagnostic tools for the wine industry.

Fisher information for smart sampling in time-domain spectroscopy.

Time-domain spectroscopy encompasses a wide range of techniques, such as Fourier-transform infrared, pump-probe, Fourier-transform Raman, and two-dimensional electronic spectroscopies. These methods enable various applications, such as molecule characterization, excited state dynamics studies, or spectral classification. Typically, these techniques rarely use sampling schemes that exploit the prior knowledge scientists typically have before the actual experiment. Indeed, not all sampling coordinates carry the same amount of information, and a careful selection of the sampling points may notably affect the resulting performance. In this work, we rationalize, with examples, the various advantages of using an optimal sampling scheme tailored to the specific experimental characteristics and/or expected results. We show that using a sampling scheme optimizing the Fisher information minimizes the variance of the desired parameters. This can greatly improve, for example, spectral classifications and multidimensional spectroscopy. We demonstrate how smart sampling may reduce the acquisition time of an experiment by one to two orders of magnitude, while still providing a similar level of information.

The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings.

Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.

Coherent Vibrations Promote Charge-Transfer across a Graphene-Based Interface.

Discerning the impact of the coherent motion of the nuclei on the timing and efficiency of charge transfer at the donor-acceptor interface is essential for designing performance-enhanced optoelectronic devices. Here, we employ an experimental approach using photocurrent detection in coherent multidimensional spectroscopy to excite a donor aromatic macrocycle and collect the charge transferred to a 2D acceptor layer. For this purpose, we prepared a cobalt phthalocyanine-graphene (CoPc-Gr) interface. Unlike blends, the well-ordered architecture achieved through the physical separation of the two layers allows us to unambiguously collect the electrical signal from graphene alone and associate it with a microscopic understanding of the whole process. The CoPc-Gr interface exhibits an ultrafast electron-transfer signal, stemming from an interlayer mechanism. Remarkably, the signal presents an oscillating time evolution modulated by coherent vibrations originating from the laser-excited CoPc states. By performing Fourier analysis on the beatings and correlating it with the Raman features, along with a comprehensive first-principles characterization of the vibrational coupling in the CoPc excited states, we successfully identify both the orbitals and molecular vibrations that promote the charge transfer at the interface.

Vibronic Coupling Drives the Ultrafast Internal Conversion in a Functionalized Free-Base Porphyrin.

Internal conversion (IC) is a common radiationless transition in polyatomic molecules. Theory predicts that molecular vibrations assist IC between excited states, and ultrafast experiments can provide insight into their structure-function relationship. Here we elucidate the dynamics of the vibrational modes driving the IC process within the Q band of a functionalized porphyrin molecule. Through a combination of ultrafast multidimensional spectroscopies and theoretical modeling, we observe a 60 fs Qy-Qx IC and demonstrate that it is driven by the interplay among multiple high-frequency modes. Notably, we identify 1510 cm-1 as the leading tuning mode that brings the porphyrin to an optimal geometry for energy surface crossing. By employing coherent wave packet analysis, we highlight a set of short-lived vibrations (1200-1400 cm-1), promoting the IC within ≈60 fs. Furthermore, we identify one coupling mode (1350 cm-1) that is responsible for vibronic mixing within the Q states. Our findings indicate that porphyrin-core functionalization modulates IC effectively, offering new opportunities in photocatalysis and optoelectronics.

Liquid crystal wave plate operating close to 18 THz.

Controlling the properties of mid- and far-infrared radiation can provide a means to transiently alter the properties of materials for novel applications. However, a limited number of optical elements are available to control its polarization state. Here we show that a 15-µm thick liquid crystal cell containing 8CB (4-octyl-4'-cyanobiphenyl) in the ordered, smectic A phase can be used as a phase retarder or wave plate. This was tested using the bright, short-pulsed (∼1 ps) radiation centered at 16.5 µm (18.15 THz) that is emitted by a free electron laser at high repetition rate (13 MHz). These results demonstrate a possible tool for the exploration of the mid- and far-infrared range and could be used to develop novel metamaterials or extend multidimensional spectroscopy to this portion of the electromagnetic spectrum.

Multidimensional Spectroscopy of Nuclear Spin Clusters in Diamond.

Optically active spin defects in solids offer promising platforms to investigate nuclear spin clusters with high sensitivity and atomic-site resolution. To leverage near-surface defects for molecular structure analysis in chemical and biological contexts using nuclear magnetic resonance (NMR), further advances in spectroscopic characterization of nuclear environments are essential. Here, we report Fourier spectroscopy techniques to improve localization and mapping of the test bed ^{13}C nuclear spin environment of individual, shallow nitrogen-vacancy centers at room temperature. We use multidimensional spectroscopy, well-known from classical NMR, in combination with weak measurements of single-nuclear-spin precession. We demonstrate two examples of multidimensional NMR: (i)improved nuclear spin localization by separate encoding of the two hyperfine components along spectral dimensions and (ii)spectral editing of nuclear-spin pairs, including measurement of internuclear coupling constants. Our work adds important tools for the spectroscopic analysis of molecular structures by single-spin probes.

Hiding in plain sight: Complex interaction patterns between Tau and 14-3-3ζ protein variants

Tau protein is an intrinsically disordered protein that plays a key role in Alzheimer's disease (AD). In brains of AD patients, Tau occurs abnormally phosphorylated and aggregated in neurofibrillary tangles (NFTs). Together with Tau, 14-3-3 proteins – abundant cytosolic dimeric proteins – were found colocalized in the NFTs. However, so far, the molecular mechanism of the process leading to pathological changes in Tau structure as well as the direct involvement of 14-3-3 proteins are not well understood. Here, we aimed to reveal the effects of phosphorylation by protein kinase A (PKA) on Tau structural preferences and provide better insight into the interaction between Tau and 14-3-3 proteins. We also addressed the impact of monomerization-inducing phosphorylation of 14-3-3 at S58 on the binding to Tau protein. Using multidimensional nuclear magnetic resonance spectroscopy (NMR), chemical cross-linking analyzed by mass spectrometry (MS) and PAGE, we unveiled differences in their binding affinity, stoichiometry, and interfaces with single-residue resolution. We revealed that the interaction between 14-3-3 and Tau proteins is mediated not only via the 14-3-3 amphipathic binding grooves, but also via less specific interactions with 14-3-3 protein surface and, in the case of monomeric 14-3-3, also partially via the exposed dimeric interface. In addition, the hyperphosphorylation of Tau changes its affinity to 14-3-3 proteins. In conclusion, we propose quite complex interaction mode between the Tau and 14-3-3 proteins.

Multidimensional high-harmonic echo spectroscopy: Resolving coherent electron dynamics in the EUV regime

We theoretically propose a multidimensional high-harmonic echo spectroscopy technique which utilizes strong optical fields to resolve coherent electron dynamics spanning an energy range of multiple electronvolts. Using our recently developed semi-perturbative approach, we can describe the coherent valence electron dynamics driven by a sequence of phase-matched and well-separated short few-cycle strong infrared laser pulses. The recombination of tunnel-ionized electrons by each pulse coherently populates the valence states of a molecule, which allows for a direct observation of its dynamics via the high harmonic echo signal. The broad bandwidth of the effective dipole between valence states originated from the strong-field excitation results in nontrivial ultra-delayed partial rephasing echo, which is not observed in standard two-dimensional optical spectroscopic techniques in a two-level molecular systems. We demonstrate the results of simulations for the anionic molecular system and show that the ultrafast valence electron dynamics can be well captured with femtosecond resolution.

A Quantum Algorithm from Response Theory: Digital Quantum Simulation of Two-Dimensional Electronic Spectroscopy.

Multidimensional optical spectroscopies are powerful techniques to investigate energy transfer pathways in natural and artificial systems. Because of the high information content of the spectra, numerical simulations of the optical response are of primary importance to assist the interpretation of spectral features. However, the increasing complexity of the investigated systems and their quantum dynamics call for the development of novel simulation strategies. In this work, we consider using digital quantum computers. By combining quantum dynamical simulation and nonlinear response theory, we present a quantum algorithm for computing the optical response of molecular systems. The quantum advantage stems from the efficient quantum simulation of the dynamics governed by the molecular Hamiltonian, and it is demonstrated by explicitly considering exciton-vibrational coupling. The protocol is tested on a near-term quantum device, providing the digital quantum simulation of the linear and nonlinear response of simple molecular models.

Fully Phase-Locked Fiber Dual Comb Enables Accurate Frequency and Phase Detection in Multidimensional Coherent Spectroscopy

Fully Phase-Locked Fiber Dual Comb Enables Accurate Frequency and Phase Detection in Multidimensional Coherent Spectroscopy

Strategies for phase matching control in a multidimensional Floquet state spectroscopy.

Floquet state spectroscopy is an optical analogue of multiple quantum coherence nuclear magnetic resonance (MQC-NMR). Tunable ultrafast excitation pulses resonantly excite multiple states in a sample to form the Floquet state. The Floquet state emits multiple coherent beams at frequencies and in directions that conserve energy and momenta. The different output beams differ in the time ordering and coherences created by the excitation beams. They correspond to the different methodologies in the NMR family. Isolating a specific beam and monitoring the output intensity as a function of excitation frequencies creates multidimensional spectra containing cross-peaks between coupled states. The frequency range of the multidimensional spectra is limited by phase matching constraints. This paper presents a new, to the best of our knowledge, active phase matching strategy that increases the versatility of multidimensional Floquet state spectroscopy through both longer sample path lengths and larger spectral ranges.

Two-dimensional electronic spectroscopy from first principles

The recent development of multidimensional ultrafast spectroscopy techniques calls for the introduction of computational schemes that allow for the simulation of such experiments and the interpretation of the corresponding results from a microscopic point of view. In this work, we present a general and efficient first-principles scheme to compute two-dimensional electronic spectroscopy maps based on real-time time-dependent density-functional theory. The interface of this approach with the Ehrenfest scheme for molecular dynamics enables the inclusion of vibronic effects in the calculations based on a classical treatment of the nuclei. The computational complexity of the simulations is reduced by the application of numerical advances such as branching techniques, undersampling, and a novel reduced phase cycling scheme, applicable for systems with inversion symmetry. We demonstrate the effectiveness of this method by applying it to prototypical molecules such as benzene, pyridine, and pyrene. We discuss the role of the approximations that inevitably enter the adopted theoretical framework and set the stage for further extensions of the proposed method to more realistic systems.

Multidimensional coherent spectroscopy of light-driven states and their collective modes in multiband superconductors

Multidimensional coherent spectroscopy of light-driven states and their collective modes in multiband superconductors

Fast and accurate identification of pathogenic bacteria using excitation-emission spectroscopy and machine learning.

Fast and reliable identification of pathogenic bacteria is of upmost importance to human health and safety. Methods that are currently used in clinical practice are often time consuming, require expensive equipment, trained personnel, and therefore have limited applications in low resource environments. Molecular identification methods address some of these shortcomings. At the same time, they often use antibodies, their fragments, or other biomolecules as recognition units, which makes such tests specific to a particular target. In contrast, array-based methods use a combination of reporters that are not specific to a single pathogen. These methods provide a more data-rich and universal response that can be used for identification of a variety of bacteria of interest. In this report, we demonstrate the application of the excitation-emission spectroscopy of an environmentally sensitive fluorescent dye for identification of pathogenic bacterial species. 2-(4'-Dimethylamino)-3-hydroxyflavone (DMAF) interacts with the bacterial cell envelope resulting in a distinct spectral response that is unique to each bacterial species. The dynamics of dye-bacteria interaction were thoroughly investigated, and the limits of detection and identification were determined. Neural network classification algorithm was used for pattern recognition analysis and classification of spectral data. The sensor successfully discriminated between eight representative pathogenic bacteria, achieving a classification accuracy of 85.8% at the species level and 98.3% at the Gram status level. The proposed method based on excitation-emission spectroscopy of an environmentally sensitive fluorescent dye is a powerful and versatile diagnostic tool with high accuracy in identification of bacterial pathogens.

Advances in free-electron-laser based scattering techniques and spectroscopic methods

&lt;sec&gt;In 2005, the FLASH soft X-ray free-electron laser (FEL) in Hamburg, Germany, achieved its first lasing, which began an intensive phase of global FEL construction. Subsequently, the United States, Japan, South Korea, China, Italy, and Switzerland all began building such photon facilities. Recently, the new generation of FEL has started to utilize superconducting acceleration technology to achieve high-repetition-rate pulse output, thereby improving experimental efficiency. Currently completed facility is the European XFEL, ongoing constructions are the LCLS-II in the United States and the SHINE facility in Shanghai, and the facility in preparation is the Shenzhen superconducting soft X-ray free-electron laser (S&lt;sup&gt;3&lt;/sup&gt;FEL).&lt;/sec&gt;&lt;sec&gt;These FEL facilities generate coherent and tunable ultrashort pulses ranging from the extreme ultraviolet to hard X-ray spectrum, which advances the FEL-based scattering techniques such as ultrafast X-ray scattering, spectroscopy, and X-ray nonlinear optics, thereby transforming the way we study correlated quantum materials on an ultrafast timescale.&lt;/sec&gt;&lt;sec&gt;The self-amplified spontaneous emission (SASE) process in FEL leads to timing jitter between FEL pulses and the synchronized pump laser, influencing the accuracy of ultrafast time-resolved measurements. To address this issue, timing tools have been developed to measure these jitters and reindexed each pump-probe signal after measurement. This success enables ultrafast X-ray diffraction (UXRD) to be first realized, and a systematic study of Peierls distorted materials is demonstrated. In addition, the high flux of FEL pulses enables Fourier transform inelastic X-ray scattering (FT-IXS) method, which can extract the phonon dispersion curve of the entire Brillouin zone by performing the Fourier transform on the measured momentum dependent coherent phonon scattering signals, even when the system is in a non-equilibrium state.&lt;/sec&gt;&lt;sec&gt;The UXRD is typically used to study ultrafast lattice dynamics, which requires hard X-ray wavelengths. In contrast, time resolved resonant elastic X-ray scattering (tr-REXS) in the soft X-ray regime has become a standard method of investigating nano-sized charge and spin orders in correlated quantum materials on an ultrafast time scale.&lt;/sec&gt;&lt;sec&gt;In correlated quantum materials, the interplay between electron dynamics and lattice dynamics represents another important research direction. In addition to Zhi-Xun Shen's successful demonstration of the combined tr-ARPES and UXRD method at SLAC, this paper also reports the attempts to integrate UXRD with resonant X-ray emission spectroscopy (RXES) for the simultaneous measurement of electronic and lattice dynamics.&lt;/sec&gt;&lt;sec&gt;Resonant inelastic X-ray scattering (RIXS) is a powerful tool for studying elementary and collective excitations in correlated quantum materials. However, in FEL-based soft X-ray spectroscopy, the wavefront tilt introduced by the widely used grating monochromators inevitably stretches the FEL pulses, which degrades the time resolution. Therefore, the new design at FEL beamlines adopts low line density gratings with long exit arms to reduce pulse stretch and achieve relatively high energy resolution. For example, the Heisenberg-RIXS instrument at the European XFEL achieves an energy resolution of 92 meV at the Cu L&lt;sub&gt;3&lt;/sub&gt; edge and approximately 150 fs time resolution.&lt;/sec&gt;&lt;sec&gt;In recent years, scientists at SwissFEL’s Furka station have drawn inspiration from femtosecond optical covariance spectroscopy to propose a new method of generating two-dimensional time-resolved resonant inelastic X-ray scattering (2D tr-RIXS) spectra. This method involves real-time detection of single-shot FEL incident and scattered spectra, followed by deconvolution calculation to avoid photon waste and wavefront tilt caused by monochromator slits. The SQS experimental station at European XFEL, built in 2023, features a 1D-XUV spectrometer that utilizes subtle variations in photon energy absorption across the sample to induce spatial energy dispersion. Using Wolter mirrors, it directly images spatially resolved fluorescence emission from the sample onto the detector to generate 2D tr-RIXS spectra without the need for deconvolution. However, this design is limited to specific samples. Currently, the S&lt;sup&gt;3&lt;/sup&gt;FEL under designing has a novel 2D tr-RIXS instrument that uses an upstream low line density grating monochromator to generate spatial dispersion of the beam spot, allowing the full bandwidth of SASE to project spatially dispersed photon energy onto the sample. Subsequently, an optical design similar to the 1D-XUV spectrometer will be employed to achieve 2D tr-RIXS spectra, thereby expanding the applicability beyond specific liquid samples. These new instruments are designed to minimize pulse elongation by fully utilizing SASE’s full bandwidth, approaching Fourier-transform-limited RIXS spectra in both time and energy resolution.&lt;/sec&gt;&lt;sec&gt;Nonlinear X-ray optical techniques, such as sum-frequency generation (SFG) and second-harmonic generation, are adapting to X-ray wavelengths and opening up new avenues for detecting elementary excitations. The X-ray transient grating spectroscopy extends its capabilities to studying charge transport and spin dynamics on an ultrafast timescale. The future development of these scattering methods provides unique opportunities for detecting dynamical events in various systems, including surface and interface processes, chirality, nanoscale transport, and so-called multidimensional core-level spectroscopy.&lt;/sec&gt;