Vibrational Probe Research Articles

Non-negligible Axial Ligand Effect on Electrocatalytic CO2 Reduction with Iron Porphyrin Complexes

Iron(III) porphyrin complexes have been demonstrated as one of the efficient molecular catalysts for the electrochemical reduction of CO2. However, the role of axial ligands coordinated with a metal center in the complex on the electrochemical CO2 reduction activity has not been fully explored yet. Herein, iron(III) tetraphenylporphyrin thiocyanate (FeTPP-SCN) is synthesized from a commercially available catalyst of FeTPP-Cl by a counteranion exchanging reaction. Cyclic voltammetry measurements showed that the catalytic activity of FeTPP-SCN is noticeably suppressed in the DMF solutions. The structural dynamics of the axial ligand in FeTPP-SCN are further examined by the FTIR and ultrafast IR spectroscopies, where the SCN ligand is employed as the local vibrational probe. Vibrational relaxation measurements showed that the reorientational dynamics of SCN ligands was strongly restricted in DMF solution, suggesting that the subtle electrostatic interaction between the ligands and metal center in the complex can have a non-negligible effect on its catalytic activity.

Molecular Simulation-Guided Spectroscopy of Imidazolium-Based Ionic Liquids and Effects of Methylation on Ion-Cage and -Pair Dynamics.

Classical molecular dynamics simulations were performed to assess an atomistic interpretation of the ion-probe structural interactions in two typical ionic liquids (ILs), 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [BMIm][NTf2] and 1-butyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide [BDimIm][NTf2] through computational ultrafast spectroscopy. The nitrile stretching vibrations of the thiocyanate anion, [SCN]-, serve as the local mode of the ultrafast system dynamics within the imidazolium-based ionic liquid environment. The wavelet transform of classical trajectories determines the time-varying fluctuating frequencies and the stretch spectral signatures of SCN- in the normalized distribution. However, computational modeling of the two-dimensional (2D) spectra from the wavelet-derived vibrational frequencies yields time evolution of the local molecular structure along with the varied time-dependent dynamics of the spectral diffusion process. We calculated the frequency-frequency correlation functions (FFCFs), time correlations associated with the ion-pair and -cage dynamics, and mean square displacements as a function of time, depicting diffusive dynamics. The calculated results based on the pair correlation functions and the distribution of atomic density suggest that the hydrogen and methylated carbon at the two-position of the imidazolium ring of [BMIm] and [BDimIm] cations, respectively, strongly interact with the probe through the N of the thiocyanate anion rather than the S atom. The center-of-mass center-of-mass (COM-COM) cation-probe radial distribution functions (RDFs) in conjunction with the site-specific structural analysis further reveal well-structured interactions of the thiocyanate ion and [BMIm]+ cation rather than the [BDimIm] cation. In contrast, the anion-probe COM-COM RDFs depict weak interactive associations within the vibrational probe [SCN]- and [NTf2]- ions. Methylation at the two-position of the imidazolium ring predicts slower structural reorganization and breaking and reformation dynamics of the ion pairs and cages within the ionic liquid framework.

(Invited) In Situ Time-Resolved Vibrational Spectroscopic Probe of Catalyst Structures, Dynamics and Reaction Mechanisms on Semiconductor Photoelectrodes

Attachment of molecular catalysts onto semiconductor or metal electrodes is a promising approach for rational design of efficient photoelectrochemical cells for solar water splitting and CO2 reduction. The understanding and improvement of such devices requires fundamental understanding of the structure and dynamics of catalysts as well as the interfacial electrolyte environment at electrode-liquid interfaces. Vibrational sum frequency generation (VSFG) spectroscopy is an in situ interface specific technique for probing interfacial properties at the semiconductor electrode/electrolyte interface at the molecular level. In this talk, we discuss our recent efforts in developing and applying in situ time-resolved VSFG for studying structural and dynamics of rhenium bipyridyl and other molecular CO2 reduction catalysts on semiconductor and metal electrodes. We have shown that by combining VSFG experiment with advanced computational modeling, catalyst adsorption geometry can be determined; through electrochemical Stark effect, local electric field and the potential profile in the electric double layer under light and dark conditions can be directly measured; using VSFG as a time-dependent probe, the interfacial charge transfer dynamics can be directly measured and key reactive intermediates can be identified.

Multiple Ensembles of the Hydrogen-bonded Network in Ethylammonium Nitrate versus Water from Vibrational Spectral Dynamics of SCN- Probe.

We performed classical molecular dynamics simulations to monitor the structural interactions and ultrafast dynamical and spectral response in the protic ionic liquid, ethylammonium nitrate (EAN) and water using the nitrile stretching mode of thiocyanate ion (SCN- ) as the vibrational probe. The normalized frequency distribution of the nitrile stretch in SCN- attains an asymmetric shape in EAN, indicating the existence of more than one hydrogen-bonding environment in EAN. Further, we computed the 2D IR spectrum from classical trajectories, applying the response function formalism. Spectral diffusion dynamics in EAN undergo an initial rattling of the SCN- inside the local ion-cage occurring at a timescale of 0.10 ps, followed by the breakup of the ion-cage activating molecular diffusion at 7.86 ps timescale. In contrast, the dynamics of structural reorganization occur at a timescale of 0.58 ps in H2 O. Hence, the time dependence of the frequency-frequency correlation function decay hints at the local molecular structure and ultrafast ion dynamics of the SCN- probe. The loss of frequency correlation read from the peak shape changes in the 2D correlation spectrum as a function of waiting time is faster in H2 O than in EAN due to the enhanced structural ordering and higher viscosity of the latter. We provide an atomic-level interpretation of the solvation environment around SCN- in EAN and water, which indicates multiple ensembles of the hydrogen bond network in EAN.

Water Dynamics in Aqueous Poly-N-Isopropylacrylamide Below and Through the Lower Critical Solution Temperature.

Poly-N-isopropylacrylamide (PNIPAM) is a thermo-responsive polymer that exhibits a reversible structural change from extended chains to aggregates in aqueous solution above its lower critical solution temperature (LCST). Using polarization-selective IR pump-probe spectroscopy, the water orientational dynamics in PNIPAM from below to above the LCST were examined and compared to those of its monomer solution, N-isopropylacrylamide (NIPAM), polyacrylamide, and an acrylamide monomer solution, which are not thermo-responsive. The OD stretch of dilute HOD in H2O is used as a vibrational probe of water orientational dynamics. Below the LCST of the polymer, NIPAM and PNIPAM solutions exhibited identical water dynamics that were significantly different from those of bulk water, containing both faster and slower components due to solute-water interactions. Therefore, there is no difference in the nature of water interactions with a single NIPAM moiety and a long polymer chain. For all systems, including PNIPAM below and above the LCST, the orientational dynamics were modeled with a bulk water component and a polymer/monomer-associated component based on previous experimental and computational findings. Above the LCST, PNIPAM showed fast water orientational relaxation but much slower long-time dynamics compared to those of NIPAM. The slow component in PNIPAM, which was too slow to be accurately measured due to the limited OD vibrational lifetime, is ascribed to water confined in small voids (<2 nm in diameter) of PNIPAM globules. These results highlight important details about thermo-responsive polymers and the dynamics of their solvation water as they undergo a significant structural change.

The 2022 Emerging Leader in Molecular Spectroscopy Award

This year’s molecular spectroscopy award recipient is Lu Wei, an assistant professor of chemistry at the California Institute of Technology in Pasadena, California. From her days as a graduate student at Columbia University, Wei’s work has focused on the development and application of stimulated Raman scattering (SRS) microscopy for bioanalysis, spectroscopy-informed design of vibrational imaging probes, and sample-engineering strategies.

Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations.

We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.

Structure and Interaction of Ceramide-Containing Liposomes with Gold Nanoparticles as Characterized by SERS and Cryo-EM.

Due to the great potential of surface-enhanced Raman scattering (SERS) as local vibrational probe of lipid-nanostructure interaction in lipid bilayers, it is important to characterize these interactions in detail. The interpretation of SERS data of lipids in living cells requires an understanding of how the molecules interact with gold nanostructures and how intermolecular interactions influence the proximity and contact between lipids and nanoparticles. Ceramide, a sphingolipid that acts as important structural component and regulator of biological function, therefore of interest to probing, lacks a phosphocholine head group that is common to many lipids used in liposome models. SERS spectra of liposomes of a mixture of ceramide, phosphatidic acid, and phosphatidylcholine, as well as of pure ceramide and of the phospholipid mixture are reported. Distinct groups of SERS spectra represent varied contributions of the choline, sphingosine, and phosphate head groups and the structures of the acyl chains. Spectral bands related to the state of order of the membrane and moreover to the amide function of the sphingosine head groups indicate that the gold nanoparticles interact with molecules involved in different intermolecular relations. While cryogenic electron microscopy shows the formation of bilayer liposomes in all preparations, pure ceramide was found to also form supramolecular, concentric stacked and densely packed lamellar, nonliposomal structures. That the formation of such supramolecular assemblies supports the intermolecular interactions of ceramide is indicated by the SERS data. The unique spectral features that are assigned to the ceramide-containing lipid model systems here enable an identification of these molecules in biological systems and allow us to obtain information on their structure and interaction by SERS.

Anomalous Infrared Absorbance of S═O: A Perturbation Study of α-C-H/D.

Solvatochromic shifts of S═O vibrational probes describe the strength of the surrounding electric fields and the hydrogen bonding status. Herein, we demonstrated how the solvents alter the infrared (IR) spectra of the S═O vibrating mode. The experimental measurement of the involvement of α-H/D isotopic interactions with different solvents and their effects on the IR absorbance spectra of the vibrational probe provides detailed knowledge of the microsolvation environment despite the complexity of overlapping bands in the spectra. Herein, we discover how the solvents interact differently with DMSO and DMSO-d6, while being electronically and structurally the same. Interestingly, the IR spectrum of the S═O mode remains unaltered during α-isotopic replacement in the presence of aprotic solvents (acetone, acetonitrile, and dichloromethane), but in strongly coordinating polar solvents (D2O), it is altered remarkably. There is a lack of quantitative information about the influence of the α-H atom or α-isotopic substitution on the vibrational probe in the literature. Our experiments provide a detailed molecular understanding of the structure of DMSO in DMSO-solvent binary mixtures. As DMSO plays an important role in virtually all subdisciplines of chemistry and biology, we believe that our work will be of interest to a large diversity of studies in these fields.

Wavelength-multiplexed hook nanoantennas for machine learning enabled mid-infrared spectroscopy

Infrared (IR) plasmonic nanoantennas (PNAs) are powerful tools to identify molecules by the IR fingerprint absorption from plasmon-molecules interaction. However, the sensitivity and bandwidth of PNAs are limited by the small overlap between molecules and sensing hotspots and the sharp plasmonic resonance peaks. In addition to intuitive methods like enhancement of electric field of PNAs and enrichment of molecules on PNAs surfaces, we propose a loss engineering method to optimize damping rate by reducing radiative loss using hook nanoantennas (HNAs). Furthermore, with the spectral multiplexing of the HNAs from gradient dimension, the wavelength-multiplexed HNAs (WMHNAs) serve as ultrasensitive vibrational probes in a continuous ultra-broadband region (wavelengths from 6 μm to 9 μm). Leveraging the multi-dimensional features captured by WMHNA, we develop a machine learning method to extract complementary physical and chemical information from molecules. The proof-of-concept demonstration of molecular recognition from mixed alcohols (methanol, ethanol, and isopropanol) shows 100% identification accuracy from the microfluidic integrated WMHNAs. Our work brings another degree of freedom to optimize PNAs towards small-volume, real-time, label-free molecular recognition from various species in low concentrations for chemical and biological diagnostics.

Ion Depletion in the Interfacial Microenvironment from Cell-Surface Interactions.

The nanoscale region immediately adjacent to surfaces, although challenging to probe, is directly responsible for local chemical and physical interactions between a material and its surroundings. Cell-surface contacts are mediated by a combination of electrostatic and acid-base interactions that alter the local environment over time. In this study, a label-free vibrational probe with a nanometer length scale reveals that the electrostatic potential at a silica surface gradually increases in the presence of bacteria in solution. We illustrate that the cells themselves are not responsible for this effect. Rather, they alter the interfacial chemical environment in a manner that is consistent with a reduction of the ionic strength to a level that is roughly four times lower than that of the bulk aqueous phase.

On-Off Infrared Absorption of the S═O Vibrational Probe of Dimethyl Sulfoxide.

Dimethyl sulfoxide (DMSO), a polar solvent molecule, is used in a wide range of therapeutic and pharmacological applications. Different intermolecular interactions, such as dimerization and hydrogen bonding with water, are crucial to understanding the role of DMSO in applications. Herein, we study DMSO in various solvation environments to decipher the environment-dependent dimerization and hydrogen-bonding propensity. We use a combination of infrared spectroscopy, quantum mechanical calculations, and molecular dynamics simulations to reach our conclusions. Although DMSO can exist in a dynamic equilibrium between monomers and dimers, our results show that the relative intensity of the S═O stretch and the CH3 rocking modes is a spectroscopic indicator of the extent of DMSO dimerization in solution. The dimerization (self-association) is seen to be maximum in neat DMSO. When dissolved in different solvents, the dimerization propensity decreases with increasing solvent polarity. In the presence of a protic solvent, such as water, DMSO forms a hydrogen bond with the solvent molecules, thereby reducing the extent of dimerization. Further, we estimate the hydrogen-bond occupancy of DMSO. Our results show that DMSO predominantly exists as doubly hydrogen-bonded in water.

Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra.

Ultrafast spectroscopy often involves measuring weak signals and long data acquisition times. Spectra are typically collected as a "pump-probe" spectrum by measuring differences in intensity across laser shots. Shot-to-shot intensity fluctuations are most often the primary source of noise in ultrafast spectroscopy. Here, we present a novel approach for denoising ultrafast two-dimensional infrared (2D IR) spectra using conditional generative adversarial neural networks (cGANNs). The cGANN approach is able to eliminate shot-to-shot noise and reconstruct the line shapes present in the noisy input spectrum. We present a general approach for training the cGANN using matched pairs of noisy and clean synthetic 2D IR spectra based on the Kubo-line shape model for a three-level system. Experimental shot-to-shot laser noise is added to synthetic spectra to recreate the noise profile present in measured experimental spectra. The cGANNs can recover line shapes from synthetic 2D IR spectra with signal-to-noise ratios as low as 2:1, while largely preserving the key features such as center frequencies, line widths, and diagonal elongation. In addition, we benchmark the performance of the cGANN using experimental 2D IR spectra of an ester carbonyl vibrational probe and demonstrate that, by applying the cGANN denoising approach, we can extract the frequency-frequency time correlation function (FFCF) from reconstructed spectra using a nodal-line slope analysis. Finally, we provide a set of practical guidelines for extending the denoising method to other coherent multidimensional spectroscopies.

A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site.

The catalytic power of an electric field depends on its magnitude and orientation with respect to the reactive chemical species. Understanding and designing new catalysts for electrostatic catalysis thus requires methods to measure the electric field orientation and magnitude at the molecular scale. We demonstrate that electric field orientations can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect of both the C=O and C-D stretches of a deuterated aldehyde. Combining spectroscopy with molecular dynamics and electronic structure partitioning methods, we demonstrate that, despite distinct polarities, solvents act similarly in their preference for electrostatically stabilizing large bond dipoles at the expense of destabilizing small ones. In contrast, we find that for an active-site aldehyde inhibitor of liver alcohol dehydrogenase, the electric field orientation deviates markedly from that found in solvents, which provides direct evidence for the fundamental difference between the electrostatic environment of solvents and that of a preorganized enzyme active site.

Vibrational probes of anharmonic interactions in the molecular ferroelectric 2-methylbenzimidazole

We report experimental and computational characterization of the anharmonic interactions between the constituents of the molecular ferroelectric material 2-methylbenzimi-dazole (MBI). Using experimental Raman spectroscopy measurements across a wide range of temperatures we assess the anharmonic properties of this material’s vibrations we expect to play a major role in proton tautomerism (PT) mechanism that explain ferroelectric switching in MBI. Through an application of the standard theory of anharmonic contributions to the interatomic potential energy of MBI we develop and apply a method to decipher how cubic and quartic anharmonic coupling to low frequency lattice vibrations affect the frequency of an intramolecular ring vibration of the molecular constituents of this material capable of modulating carbon-nitrogen double bonds that alternate in the PT mechanism. In addition, we use the theory of vibrational solitons to show the appearance of satellites peaks red-shifted from the N-H stretching vibration of MBI stem from self-trapped vibron states. We assess the number of these trapped states and the modes along which trapping occurs to show MBI possesses distinct phases in which excitations of the N-H stretching vibration couple to different low frequency lattice vibrational modes. We propose increased N-H stretching vibrational trapping at low temperature helps explain reductions in the temperature-dependent dielectric constant of MBI measured previously. These results highlight the important role vibrational spectroscopy can play in understanding how intermolecular interactions impact the structural dynamics of materials central to sustainable information storage and nonlinear optical technologies

Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments.

Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C≡N bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.

Dynamics in tris(pentafluoroethyl)trifluorophosphate (FAP) anion based ionic liquids: A 2D-IR study with tungsten hexacarbonyl

Ultrafast two-dimensional infrared spectroscopy (2D-IR) measurements for tungsten hexacarbonyl, W(CO)6, has been performed in two fluoroalkylphosphate ([FAP])-based ultrahigh hydrophobic, ionic liquids, namely, 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)-trifluorophosphate ([EMIM][FAP]) and 1-(hexyl)-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([HMIM][FAP]) to probe their local structure and dynamics. To understand the effect of FAP anion on the dynamics, a relatively less hydrophobic [PF6-] anion has been introduced in the form of [HMIM][PF6]. While the linear IR spectra records some influence of anion in terms of spectral shifts, the alkyl chain length of the cation seems to have no significant influence on the spectral peak position; and even the spectral broadening is found to be in the similar range. Further, vibrational population relaxation dynamics and vibrational anisotropy decay also does not show any significant variation due to difference in constituent of these ionic liquids as well as its solvent properties, such as, viscosity. Finally, 2D-IR spectra show large variation in the spectral shapes with waiting times, which qualitatively remains similar in all the tested ionic liquids. The frequency-fluctuation correlation function measured from 2D-IR spectra displays a bi-exponential decay with the shorter time-constant dependent on the identity of the anion, and has been attributed to the ion-rattling motion, whereas, the longer component has been found to be invariant with the identity of ionic liquid, and has been attributed to ion-cage motions which is in line with previous MD simulations as well as previous experimental measurements, using ionic vibrational probe. Overall, 2D-IR spectroscopy, in combination with this neutral and hydrophobic probe, W(CO)6 provides a unique opportunity to understand the local structural dynamics of this ultrahigh hydrophobic ionic liquid which are otherwise not accessible by hitherto explored ionic vibrational probes.

Protein–water coupling tunes the anharmonicity of amide I modes in the interfacial membrane-bound proteins

The diagonal anharmonicity of an amide I mode of protein backbones plays a critical role in a protein's vibrational dynamics and energy transfer. However, this anharmonicity of long-chain peptides and proteins in H2O environment is still lacking. Here, we investigate the anharmonicity of the amide I band of proteins at the lipid membrane/H2O interface using a surface-sensitive pump-probe setup in which a femtosecond infrared pump is followed by a femtosecond broadband sum frequency generation vibrational spectroscopy probe. It is found that the anharmonicity of the amide I mode in ideal α-helical and β-sheet structures at hydrophobic environments is 3-4cm-1, indicating that the amide I mode in ideal α-helical and β-sheet structures is delocalized over eight peptide bonds. The anharmonicity increases as the bandwidth of the amide I mode increases due to the exposure of peptide bonds to H2O. More H2O exposure amounts lead to a larger anharmonicity. The amide I mode of the peptides with large H2O exposure amounts is localized in one to two peptide bonds. Our finding reveals that the coupling between the amide I mode and the H2O bending mode does not facilitate the delocalization of the amide I mode along the peptide chain, highlighting the impact of H2O on energy transfer and structural dynamics of proteins.

Nitrile IR intensities directly measure electric fields in protic and non-protic environments

Nitriles are useful vibrational probes; the interpretation of their frequencies, however, is complicated by hydrogen bonding in protic environments. Here we observed a vibrational Stark effect (VSE) which correlates electric field to transition dipole moment (and, by extension, the nitrile peak area) instead of to frequency. This VSE governs the transition dipole moment for the CO stretch in acetophenone and the CN stretch in benzonitrile, with studies performed in bulk-phase solvents. While modest for the acetophenone carbonyl CO, the VSE for the benzonitrile nitrile CN is dramatic, and a >300% increase in absolute peak area from hexanes to water.

A two-directional vibrational probe reveals the distinct electric field orientation at the active site of liver alcohol dehydrogenase

An increasing amount of evidence has shown that the extraordinary catalytic power of enzymes arises in part from large and pre-oriented electric fields at the active sites exerted by precisely positioned functional groups. While the field magnitudes at several enzyme’s active sites have been studied previously, the field orientation, an equally crucial quantity due to the vectorial nature of electric fields, has not been experimentally accessible despite extensive computational studies highlighting its critical role in electrostatic and enzymatic catalysis.