Single-molecule Spectra Research Articles

High-Throughput Single-Molecule Surface-Enhanced Raman Spectroscopic Profiling of Single-Amino Acid Substitutions in Peptides by a Gold Plasmonic Nanopore.

Simultaneous detection and structural characterization of protein variants on a single platform are highly desirable but technically challenging. Herein, we present a single-molecule spectral system based on a gold plasmonic nanopore for analyzing two peptides and their single-point mutated variants. The gold plasmonic nanopore enabled the high-throughput acquisition of surface-enhanced Raman scattering (SERS) spectra at the single-molecule level by electrically driving analytes into hot spots. Furthermore, a statistical method based on Boolean operations was developed to extract prominent features from fluctuated single-molecule SERS spectra. The effects of the single-amino acid substitutions on both the intramolecular interactions and the peptide conformations were directly characterized by the nanopore system, and the results agreed with the predictions by AlphaFold2. This study highlights the mutual benefits of spectroscopy and nanopore technology, whereby the gold plasmonic nanopore offers a powerful tool for the structural analysis of single-molecule proteins.

Key role of chromophore-modified vibrational modes on thermal broadening of single-molecule spectra in disordered solids

Key role of chromophore-modified vibrational modes on thermal broadening of single-molecule spectra in disordered solids

Tuning the Chirality Evolution in Achiral Subnanometer Systems by Judicious Control of Molecule Interactions.

Chirality evolution from molecule levels to the nanoscale in an achiral system is a fundamental issue that remains undiscovered. Here, we report the assembly of polyoxometalate (POM) clusters into chiral subnanostructures in achiral systems by programmable single-molecule interactions. Driven by the competing binding of Ca2+ and surface ligands, POM assemblies would twist into helical nanobelts, nanorings, and nanotubes with tunable helicity. Chiral molecules can be used to differentiate the formation energies of chiral isomers and immobilize the homochiral isomer, where strong circular dichroism (CD) signals are obtained in both solutions and films. Chiral helical nanobelts can be used as circularly polarized light (CPL) photodetectors due to their distinct chiroptic responsivity for right and left CPL. By the fine-tuning of interactions at single-molecule levels, the morphology and CD spectra of helical assemblies can be precisely controlled, providing an atomic precision model for investigation of the structure-chirality relationship and chirality manipulation at the nanoscale.

Quartz-Enhanced Photoacoustic Spectroscopy Assisted by Partial Least-Squares Regression for Multi-Gas Measurements.

We report on the use of quartz-enhanced photoacoustic spectroscopy (QEPAS) for multi-gas detection. Photoacoustic (PA) spectra of mixtures of water (H2O), ammonia (NH3), and methane (CH4) were measured in the mid-infrared (MIR) wavelength range using a mid-infrared (MIR) optical parametric oscillator (OPO) light source. Highly overlapping absorption spectra are a common challenge for gas spectroscopy. To mitigate this, we used a partial least-squares regression (PLS) method to estimate the mixing ratio and concentrations of the individual gasses. The concentration range explored in the analysis varies from a few parts per million (ppm) to thousands of ppm. Spectra obtained from HITRAN and experimental single-molecule reference spectra of each of the molecular species were acquired and used as training data sets. These spectra were used to generate simulated spectra of the gas mixtures (linear combinations of the reference spectra). Here, in this proof-of-concept experiment, we demonstrate that after an absolute calibration of the QEPAS cell, the PLS analyses could be used to determine concentrations of single molecular species with a relative accuracy within a few % for mixtures of H2O, NH3, and CH4 and with an absolute sensitivity of approximately 300 (±50) ppm/V, 50 (±5) ppm/V, and 5 (±2) ppm/V for water, ammonia, and methane, respectively. This demonstrates that QEPAS assisted by PLS is a powerful approach to estimate concentrations of individual gas components with considerable spectral overlap, which is a typical scenario for real-life adoptions and applications.

Deep learning-enhanced single-molecule spectrum imaging

Fluorescence is widely used in biological imaging and biosensing. Rich information can be revealed from the fluorescence spectrum of fluorescent molecules, such as pH, viscosity and polarity of the molecule’s environment, and distance between two FRET molecules. However, constructing the fluorescence spectrum of a single fluorescent molecule typically requires a significant number of photons, which can suffer from photobleaching and, therefore, limit its potential applications. Here, we propose a deep learning-enhanced single-molecule spectrum imaging method (SpecGAN) for improving the single-molecule spectrum imaging efficiency. In SpecGAN, the photon flux required to extract a single-molecule fluorescence spectrum can be reduced by 100 times, which enables two orders of magnitude higher temporal resolution compared to the conventional single-molecule spectrometer. The concept of SpecGAN was validated through numerical simulation and single Nile Red molecule spectrum imaging on support lipid bilayers (SLBs). With SpecGAN, the super-resolution spectrum image of the COS-7 membrane can be reconstructed with merely 12 000 frames of single-molecule localization images, which is almost half of the previously reported frame count for spectrally resolved super-resolution imaging. The low photon flux requirement and high temporal resolution of SpecGAN make it a promising tool for investigating the molecular spectrum dynamics related to biological functions or biomolecule interactions.

Crystal effects in the vibrational spectra of one-dimensional molecular spin crossover crystals using molecular dynamics simulations

We use molecular dynamics simulations to model the iron phonon density of states (pDOS) of a spin crossover (SCO) crystal built from 39-nuclear [Fe(atrz)_3Cl_2] chains (atrz = 4-amino-1,2,4-triazole). This is possible by using an atomistic potential that depends on the spin state of the Fe atoms. While quantum-chemical methods are able to provide data on isolated SCO molecules, the computational costs necessitate the use of classical simulations to calculate crystal effects on the spectra. Data are provided for a high-spin (HS) crystal, in which all Fe atoms are in their HS state, and a low-spin (LS) crystal. HS and LS crystals show distinctively different spectra that are in agreement with experimental data. Compared to the single-molecule spectra, the crystal spectra show several distinctive features: (i) The spectra are smoother, and the main peaks are slightly reduced in amplitude. (ii) The effect of intermolecular interactions shows up in additional structure at long-wavelengths. Good agreement between experimental and simulated phonon spectra is observed. The lattice-dynamics analysis of the low-energy pDOS allows to extract the temperature dependence of the vibrational entropy of the LS and HS crystals. Our study thus provides novel information about the crystal effects in SCO crystals.

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms.

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. We find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

Envemind: Accurate Monoisotopic Mass Determination Based On Isotopic Envelope

Nowadays, monoisotopic mass is used as an important feature in top-down proteomics. Knowing the exact monoisotopic mass is helpful for precise and quick protein identification in large protein databases. However, only in spectra of small molecules the monoisotopic peak is visible. For bigger molecules like proteins, it is hidden in noise or undetected at all, and therefore its position has to be predicted. By improving the prediction of the peak, we contribute to a more accurate identification of molecules, which is crucial in fields such as chemistry and medicine. In this work, we present the envemind algorithm, which is a two-step procedure to predict monoisotopic masses of proteins. The prediction is based on an isotopic envelope. Therefore, envemind is dedicated to spectra where we are able to resolve the one dalton separated isotopic variants. Furthermore, only single-molecule spectra are allowed, that is, spectra that do not require prior deconvolution. The algorithm deals with the problem of off-by-one dalton errors, which are common in monoisotopic mass prediction. A novel aspect of this work is a mathematical exploration of the space of molecules, where we equate chemical formulas and their theoretical spectrum. Since the space of molecules consists of all possible chemical formulas, this approach is not limited to known substances only. This makes optimization processes faster and enables to approximate theoretical spectrum for a given experimental one. The algorithm is available as a Python package envemind on our GitHub page https://github.com/PiotrRadzinski/envemind.

Nanoscale local hydrogen-bonding sensing using single-molecule spectroscopic imaging

Hydrogen bonds play significant roles in many chemical and biological processes. However, it remains challenging to probe the local hydrogen-bonding characters at the nanoscale. Herein, we developed a new single-molecule sensing approach to examine the nature of the local hydrogen bonding characters with surrounding molecules at the single-molecule level by employing a single-molecule spectroscopic imaging technique and a Nile blue (NB) dye as a single-molecule sensor. This method is based on the recent developments in single-molecule spectroscopic imaging that enabled local chemical property sensing at the single-molecule level, which is generally masked in the ensemble averages of bulk measurements. By observing the single-molecule fluorescence spectrum of hydrogen-bonding sensor, NB dye, under different chemical conditions, we could differentiate their hydrogen-bonding characteristics at the single-molecule level, even in the solvent mixtures. We believe that the results will be effective in probing different chemical properties of unknown solvent molecules at the single-molecule level, which could not be achieved using any previously reported method.

Influence of bulky substituents on single-molecule SERS sensitivity.

The surface-enhanced Raman spectroscopy (SERS) detection limit strongly depends on the molecular structure, which we demonstrate for a family of tert-butyl-substituted porphycenes. Even though the investigated species present very similar photophysical properties, the ratio between the SERS signal and fluorescence background depends on the number of bulky tert-butyl groups. Moreover, the probability of single molecule detection systematically drops with the number of the moieties attached to the pyrrole ring. As steric hindrance is the only significantly changing feature among the studied chromophores, we attribute the observed phenomena to the spatial structure. We also show that the sensitivity of the SERS technique can be improved by lowering the temperature. We managed to observe single-molecule spectra for derivatives for which this was unattainable at room temperature.

(Invited) Combined Single-Molecule Raman and Conductance Spectroscopies

The nanoscale manipulation and characterization of individual molecules is necessary for understanding the intricacies of molecular structure which ultimately governs phenomena such as reaction mechanisms, catalysis, local effective temperatures, surface interactions, and charge transport phenomenon. Along these lines, the field of molecular-scale electronics has evolved tremendously in recent years: from the initial experiments claiming single-molecule conductance measurements to the development of robust and reproducible platforms that have begun providing a detailed understanding of the charge transport properties of these systems. It has now become possible to probe the chemical, structural, mechanical, and electrical properties of single-molecule devices to explore unique functional paradigms for applications. However, continued advances in in situ characterization of a molecular junction are needed to provide detailed information about the molecular configuration and its impact on the charge transport, reactions, and device behavior. Single-molecule conductance and Raman spectroscopies each provide unique perspectives into the behavior of molecular systems and reactions at the single-molecule level. In this talk we will discuss the development and implementation of system designed to simultaneously obtain conductance information and Raman spectra from a molecular junction to provide this information. This will include the development of a MEMS-based break junction system that allows facile integration with a Raman microscope to maximize the solid-angle and photon collection.This multi-dimensional information yields repeatable, self-consistent, verification of single-molecule resolution, and allows for detailed analysis of structural and configurational changes of the molecule in situ. We will discuss the correlation between single-molecule binding events and changes in Raman spectra (intensity, modes, etc.) and conductance to explore the possibility of obtaining single-molecule spectra from the molecule bound between two electrodes. We will further explore the utility of this system for in situ characterization of active single-molecule devices including electrically-active single-molecule switches and memory devices.

Plasmon-Driven Motion of an Individual Molecule.

We demonstrate that nanocavity plasmons generated a few nanometers away from a molecule can induce molecular motion. For this, we study the well-known rapid shuttling motion of zinc phthalocyanine molecules adsorbed on ultrathin NaCl films by combining scanning tunneling microscopy (STM) and spectroscopy (STS) with STM-induced light emission. Comparing spatially resolved single-molecule luminescence spectra from molecules anchored to a step edge with isolated molecules adsorbed on the free surface, we found that the azimuthal modulation of the Lamb shift is diminished in case of the latter. This is evidence that the rapid shuttling motion is remotely induced by plasmon–molecule coupling. Plasmon-induced molecular motion may open an interesting playground to bridge the nanoscopic and mesoscopic worlds by combining molecular machines with nanoplasmonics to control directed motion of single molecules without the need for local probes.

Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy.

We experimentally investigated several intramolecular coordinate and environmental changes as potential causes of single-molecule fluorescence spectral heterogeneities (smFSH). We developed a high-throughput single-molecule spectroscopy method to analyze more than 5000 single-molecule emission spectra from each of 9 commonly used fluorophores with different structural rigidities and deposited on substrates with different polarities. We observed an unexpectedly high smFSH from structurally rigid Rhodamine B compared with a structurally flexible Cyanine dye-Alexa Fluor 647. Based on experimentally measured smFSH, we ruled out the system's noise uncertainty, single-molecule spectral diffusion, and environmental polarity as the primary causes of the high smFSH. We found that the rotational flexibility of N,N-dialkylated groups contributed to the smFSH. With the high smFSH observed in structurally more rigid model fluorophores, we speculated that other intramolecular coordinate and environmental changes might also contribute to the high smFSH in Rhodamines.

Ground state properties and infrared spectra of anharmonic vibrational polaritons of small molecules in cavities.

Recent experiments and theory suggest that ground state properties and reactivity of molecules can be modified when placed inside a nanoscale cavity, giving rise to strong coupling between vibrational modes and the quantized cavity field. This is commonly thought to be caused either by a cavity-distorted Born-Oppenheimer ground state potential or by the formation of light-matter hybrid states, vibrational polaritons. Here, we systematically study the effect of a cavity on ground state properties and infrared spectra of single molecules, considering vibration-cavity coupling strengths from zero up to the vibrational ultrastrong coupling regime. Using single-mode models for Li-H and O-H stretch modes and for the NH3 inversion mode, respectively, a single cavity mode in resonance with vibrational transitions is coupled to position-dependent molecular dipole functions. We address the influence of the cavity mode on polariton ground state energies, equilibrium bond lengths, dissociation energies, activation energies for isomerization, and on vibro-polaritonic infrared spectra. In agreement with earlier work, we observe all mentioned properties being strongly affected by the cavity, but only if the dipole self-energy contribution in the interaction Hamiltonian is neglected. When this term is included, these properties do not depend significantly on the coupling anymore. Vibro-polaritonic infrared spectra, in contrast, are always affected by the cavity mode due to the formation of excited vibrational polaritons. It is argued that the quantized nature of vibrational polaritons is key to not only interpreting molecular spectra in cavities but also understanding the experimentally observed modification of molecular reactivity in cavities.

Preface to the special issue dedicated to Professor Richard P. Van Duyne (1945–2019)

Preface to the special issue dedicated to Professor Richard P. Van Duyne (1945–2019)

Transient Spectral Fluctuations of Single Molecules Revealed using an Optical Antenna

Fluorescence spectra and lifetimes of single molecules reflect their specific local environments, which is not available from the ensemble-averaged measurements. Usually, a low signal-to-noise ratio of single-molecule spectroscopy impedes access to transient emission spectra of single molecules at room temperature, especially for the molecules with a low quantum yield. Here, we realize detection of transient single-molecule spectra with an effective integration time of ∼2.14 milliseconds at room temperature of methylene blue (MB) or crystal violet (CV) molecules. In the experiments, the transient emission spectra detection of single molecules is achieved through the enhanced signal using a plasmonic antenna, the suppressed background noise due to a low quantum yield, and the short dwelling time of molecular adsorption on the antenna surface. The transient spectra show apparent fluctuation in the emission intensity and shifts of the peak maximum. Interestingly, the emission spectrum presents a narrow band which can be fitted well with a single Lorentzian lineshape. The specific molecule configuration should dominate the transient spectral lineshape mainly, which is supported by the numerical ab initio simulations. These spectral fluctuations should attribute to the transitions between metastable minima in the molecular potential-energy surface. These findings provide us more understanding of the transient behaviors of single molecules at the solid-aqueous interfaces.

High-Throughput Single-Molecule Spectroscopy Resolves the Conformational Isomers of BODIPY Chromophores.

A borondipyrromethene (BODIPY) chromophore is connected to a benzoxazole, benzothiazole, or nitrobenzothiazole heterocycle through an olefinic bridge with trans configuration. Rotation about the two [C-C] bonds flanking the olefinic bridge occurs with fast kinetics in solution, leading to the equilibration of four conformational isomers for each compound. Ensemble spectroscopic measurements in solutions fail to distinguish the coexisting isomers. They reveal instead averaged absorption and emission bands with dependence of the latter on the excitation wavelength. Using high-throughput single-molecule spectroscopy, two main populations of single molecules with distinct spectral centroids are observed for each compound on glass substrates. Computational analyses suggest the two populations of molecules to be conformational isomers with antiperiplanar and periplanar arrangements of the BODIPY chromophores about its [C-C] bond to the olefinic bridge. Thus, statistical analysis of multiple single-molecule emission spectra can discriminate stereoisomers that would otherwise be impossible to distinguish by ensemble measurements alone.

Dibenzo[hi,st]ovalene as Highly Luminescent Nanographene: Efficient Synthesis via Photochemical Cyclodehydroiodination, Optoelectronic Properties, and Single-Molecule Spectroscopy.

Dibenzo[hi,st]ovalene (DBOV), as a new nanographene, has demonstrated promising optical properties, such as red emission with a high fluorescence quantum yield of 79% and stimulated emission, as well as high thermal stability and photostability, which indicated its promise as a light-emitting and optical gain material. However, the previous synthetic routes required at least 12 steps. This obstructed access to different derivatives, e.g., to obtain crystals suitable for X-ray diffraction analysis and to tune the optoelectronic properties. Here, we report an efficient synthetic pathway to DBOV based on a sequential iodination-benzannulation of bi(naphthylphenyl)diyne, followed by photochemical cyclodehydroiodination (PCDHI). This protocol included a fused bischrysene as a key intermediate and furnished scalable amounts of meso-substituted DBOV derivatives with different substituents. DBOV with 2,6-dimethylphenyl groups could be used for single-crystal X-ray analysis, revealing the precise structure of the DBOV core. The optoelectronic properties of the DBOV derivatives were investigated by UV-vis absorption and fluorescence spectroscopy, cyclic voltammetry, and density functional theory calculations. Single-molecule spectroscopy at room and low temperatures provided novel insights into the photophysics of DBOV embedded in a polymer film. As a result of weak coupling of the optical transitions to the matrix, single-molecule emission spectra at 4.5 K showed narrow vibronic lines. The fluorescence autocorrelation function covering 9 orders of magnitude in time displayed high contrast photon antibunching and bunching, from which the fluorescence decay rate and the triplet population and depopulation rates could be retrieved. Remarkably, the intersystem crossing rate into the triplet state decreased by more than an order of magnitude at low temperature, demonstrating that temperature can be a crucial parameter to boost single photon emission of an aromatic hydrocarbon.

Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge.

Single-molecule measurements have greatly enhanced our understanding of living systems. Biological systems offer nanopores, a sub-class of membrane proteins, the well-defined confined space for accommodating a single molecule. The biological nanopore acts as a single-biomolecule interface for capturing and identifying a single molecule of interest, and thus it can be used as a single-molecule sensor. In this Perspective, we focus on biological nanopore-based single-biomolecule interfaces for single-biomolecule detection. First, we outline the design of the nanopore-based single-biomolecule interface, which provides rich stochastic information regarding each biomolecule. Next, we highlight future research directions beyond DNA sequencing, including detection of rare species, identification of hidden intermediates, spectral analysis of covalent/noncovalent interactions, and tracing of the dynamic pathways of single-biopolymer behaviors. The concept of a "single-molecule ionic spectrum" is discussed, which may allow mapping of noncovalent interactions at an atomic level in the future. We also discuss the challenges and goals for the future to make this measurement possible for addressing entirely new types of biological questions, which would be an exciting area of future research.

High precision qualitative identification of yeast growth phases using molecular fusion spectra

Compared to a single molecule spectral analysis method, molecular fusion spectroscopy can obtain multi-dimensional information reflecting the target attributes more comprehensively, which makes this method have potential application value in online monitoring of microbial fermentation process. This study proposes a method based on near-infrared (NIR) and Raman molecular fusion spectroscopy for high precision identification of yeast growth phases. First, the original spectra of yeast broth were preprocessed using Savitzky-Golay (SG) convolution smoothing combined with standard normal variate (SNV). Then, a novel fusion algorithm, which was discriminant correlation analysis (DCA), was used to realize the effective fusion of the NIR and Raman spectra after preprocessing in the feature layer. Finally, a linear discriminant analysis (LDA) identification model was developed based on the DCA fusion feature vectors. The results showed that the prediction performance of the LDA identification model based on the eigenvectors by the DCA fusion is far better than the best LDA model based on the single molecule spectra, and its correct identification rate is 97.37% in the prediction set. The overall results demonstrate that molecular fusion spectroscopy can achieve high precision and rapid monitoring of yeast fermentation process, and the DCA is an effective tool for molecular spectral fusion.