Water-induced relaxation of a degenerate vibration of guanidinium using 2D IR echo spectroscopy

Vibrational anisotropy decay resolves rare earth binding induced conformational change in DTPA

Elucidating the relationship between metal-ligand interactions and the associated conformational change of the ligand is critical for understanding the separation of lanthanides via ion binding. Here we examine DTPA, a multidentate ligand that binds lanthanides, in its free and metal bound conformations using ultrafast polarization dependent vibrational spectroscopy. The polarization dependent pump-probe spectra were analyzed to extract the isotropic and anisotropic response of DTPA's carbonyl groups in the 1550-1650 cm-1 spectral region. The isotropic response reports on the population relaxation of the carbonyl stretching modes. We find that the isotropic response is influenced by the identity of the metal ion. The anisotropy decay of the carbonyl stretching modes reveals a faster decay in the lanthanide-DTPA complexes than in the free DTPA ligand. We attribute the anisotropy decay to energy transfer among the different carbonyl sites - where the conformational change results in an increased coupling between the carbonyl sites of metal-bound DTPA complexes. DFT calculations and theoretical simulations of energy transfer suggest that the carbonyl sites are more strongly coupled in the metal-bound conformations compared to the free DTPA. The stronger coupling in the metal bound DTPA conformation leads to efficient energy transfer among the different carbonyl sites. Comparing the rate of anisotropy decay across the series of metal bound DTPA complexes we find that the anisotropy is sensitive to the charge density of the central metal ion, and thus can serve as a molecular scale reporter for lanthanide ion binding.

Assessing the Role of R120 in the Gating of CrChR2 by Time-Resolved Spectroscopy from Femtoseconds to Seconds

The light-gated ion channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) is the most frequently used optogenetic tool in neurosciences. However, the precise molecular mechanism of the channel opening and the correlation among retinal isomerization, the photocycle, and the channel activity of the protein are missing. Here, we present electrophysiological and spectroscopic investigations on the R120H variant of CrChR2. R120 is a key residue in an extended network linking the retinal chromophore to several gates of the ion channel. We show that despite the deficient channel activity, the photocycle of the variant is intact. In a comparative study for R120H and the wild type, we resolve the vibrational changes in the spectral range of the retinal and amide I bands across the time range from femtoseconds to seconds. Analysis of the amide I mode reveals a significant impairment of the ultrafast protein response after retinal excitation. We conclude that channel opening in CrChR2 is prepared immediately after retinal excitation. Additionally, chromophore isomerization is essential for both photocycle and channel activities, although both processes can occur independently.

Pump Slice Amplitudes: A Simple and Robust Method for Connecting Two-Dimensional Infrared and Fourier Transform Infrared Spectra

Ultrafast two-dimensional infrared (2D IR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy are often performed in tandem, with FTIR typically used to interpret and provide hypotheses for 2D IR experiments. Comparisons between 2D IR and FTIR spectra can also be used to examine the structure and orientation in systems of coupled vibrational chromophores. The most common method for comparing 2D IR and FTIR lineshapes, the diagonal slice method, contains significant artifacts when applied to oscillators with low anharmonicities. Here, we introduce a new technique, the pump slice amplitude (PSA) method, for relating 2D IR lineshapes to FTIR lineshapes and compare PSAs against diagonal slices using theoretical and experimental spectra. We find that PSAs are significantly more similar to FTIR lineshapes than diagonal slices in systems with low anharmonicity.

Assessing the Location of Ionic and Molecular Solutes in a Molecularly Heterogeneous and Nonionic Deep Eutectic Solvent

Deep eutectic solvents (DES) are emerging sustainable designer solvents viewed as greener and better alternatives to ionic liquids. Nonionic DESs possess unique properties such as viscosity and hydrophobicity that make them desirable in microextraction applications such as oil-spill remediation. This work builds upon a nonionic DES, NMA–LA DES, previously designed by our group. The NMA–LA DES presents a rich nanoscopic morphology that could be used to allocate solutes of different polarities. In this work, the possibility of solvating different solutes within the nanoscopically heterogeneous molecular structure of the NMA–LA DES is investigated using ionic and molecular solutes. In particular, the localized vibrational transitions in these solutes are used as reporters of the DES molecular structure via vibrational spectroscopy. The FTIR and 2DIR data suggest that the ionic solute is confined in a polar and continuous domain formed by NMA, clearly sensing the direct effect of the change in NMA concentration. In the case of the molecular nonionic and polar solute, the data indicates that the solute resides in the interface between the polar and nonpolar domains. Finally, the results for the nonpolar and nonionic solute (W(CO)₆) are unexpected and less conclusive. Contrary to its polarity, the data suggest that the W(CO)₆ resides within the NMA polar domain of the DES, probably by inducing a domain restructuring in the solvent. However, the data are not conclusive enough to discard the possibility that the restructuring comprises not only the polar domain but also the interface. Overall, our results demonstrate that the NMA–LA DES has nanoscopic domains with affinity to particular molecular properties, such as polarity. Thus, the presented results have a direct implication to separation science.

Interspecies Bombolitins Exhibit Structural Diversity upon Membrane Binding, Leading to Cell Specificity

Bombolitins, a class of peptides produced by bees of the genus Bombus, target and disrupt cellular membranes, leading to lysis. Antimicrobial peptides exhibit various mechanisms of action resulting from the interplay between peptide structure, lipid composition, and cellular target membrane selectivity. Herein, two bombolitins displaying significant amino-acid-sequence similarity, BII and BL6, were assessed for antimicrobial activity as well as correlated dodecylphosphocholine (DPC) micelle binding and membrane-induced peptide conformational changes. Infrared and circular dichroism spectroscopies were used to assess the structure-function relationship of each bombolitin, and the results indicate that BII forms a rigid and helically ordered secondary structure upon binding to DPC micelles, whereas BL6 largely lacks secondary structural order. Moreover, the binding affinity of each peptide to DPC micelles was determined, revealing that BL6 displayed a difference in binding affinity by over two orders of magnitude. Further investigations into the growth-inhibitory activity of the two bombolitins were performed against Escherichia coli and Saccharomyces cerevisiae. Interestingly, BII specifically targeted S. cerevisiae, whereas BL6 more effectively inhibited E. coli growth. Overall, the antimicrobial selectivity and specificity of BII and BL6 are largely dependent on the primary as well as secondary structural content of the peptides and the membrane composition.

A comparison of the solvation structure and dynamics of the lithium ion in linear organic carbonates with different alkyl chain lengths

The structure and dynamics of electrolytes composed of lithium hexafluorophosphate (LiPF₆) in dimethyl carbonate, ethyl methyl carbonate, and diethyl carbonate were investigated using a combination of linear and two-dimensional infrared spectroscopies.

Hydration of guanidinium depends on its local environment

Hydration of gaseous guanidinium (Gdm+) with up to 100 water molecules attached was investigated using infrared photodissociation spectroscopy in the hydrogen stretch region between 2900 and 3800 cm-1. Comparisons to IR spectra of low-energy computed structures indicate that at small cluster size, water interacts strongly with Gdm+ with three inner shell water molecules each accepting two hydrogen bonds from adjacent NH2 groups in Gdm+. Comparisons to results for tetramethylammonium (TMA+) and Na+ enable structural information for larger clusters to be obtained. The similarity in the bonded OH region for Gdm(H2O)20+vs. Gdm(H2O)100+ and the similarity in the bonded OH regions between Gdm+ and TMA+ but not Na+ for clusters with <50 water molecules indicate that Gdm+ does not significantly affect the hydrogen-bonding network of water molecules at large size. These results indicate that the hydration around Gdm+ changes for clusters with more than about eight water molecules to one in which inner shell water molecules only accept a single H-bond from Gdm+. More effective H-bonding drives this change in inner-shell water molecule binding to other water molecules. These results show that hydration of Gdm+ depends on its local environment, and that Gdm+ will interact with water even more strongly in an environment where water is partially excluded, such as the surface of a protein. This enhanced hydration in a limited solvation environment may provide new insights into the effectiveness of Gdm+ as a protein denaturant.

A salt-bridge structure in solution revealed by 2D-IR spectroscopy

Salt bridges are important interactions for the stability of protein conformations, but up to now it has been difficult to determine salt-bridge geometries in solution. Here we characterize the spatial structure of a salt bridge between guanidinium (Gdm(+)) and acetate (Ac(-)) using two-dimensional vibrational (2D-IR) spectroscopy. We find that as a result of salt bridge formation there is a significant change in the infrared response of Gdm(+) and Ac(-), and cross peaks between them appear in the 2D-IR spectrum. From the 2D-IR spectrum we determine the relative orientation of the transition-dipole moments of the vibrational modes of Gdm(+) and Ac(-), as well as the coupling between them.

Quantum process tomography quantifies coherence transfer dynamics in vibrational exciton

Quantum coherence has been a subject of great interest in many scientific disciplines. However, detailed characterization of the quantum coherence in molecular systems, especially its transfer and relaxation mechanisms, still remains a major challenge. The difficulties arise in part because the spectroscopic signatures of the coherence transfer are typically overwhelmed by other excitation-relaxation processes. We use quantum process tomography (QPT) via two-dimensional infrared spectroscopy to quantify the rate of the elusive coherence transfer between two vibrational exciton states. QPT retrieves the dynamics of the dissipative quantum system directly from the experimental observables. It thus serves as an experimental alternative to theoretical models of the system-bath interaction and can be used to validate these theories. Our results for coupled carbonyl groups of a diketone molecule in chloroform, used as a benchmark system, reveal the nonsecular nature of the interaction between the exciton and the Markovian bath and open the door for the systematic studies of the dissipative quantum systems dynamics in detail.

Vibrational dynamics of a non-degenerate ultrafast rotor: the (C12,C13)-oxalate ion

Molecular ions undergoing ultrafast conformational changes on the same time scale of water motions are of significant importance in condensed phase dynamics. However, the characterization of systems with fast molecular motions has proven to be both experimentally and theoretically challenging. Here, we report the vibrational dynamics of the non-degenerate (C12,C13)-oxalate anion, an ultrafast rotor, in aqueous solution. The infrared absorption spectrum of the (C12,C13)-oxalate ion in solution reveals two vibrational transitions separated by approximately 40 cm(-1) in the 1500-1600 cm(-1) region. These two transitions are assigned to vibrational modes mainly localized in each of the carboxylate asymmetric stretch of the ion. Two-dimensional infrared spectra reveal the presence and growth of cross-peaks between these two transitions which are indicative of coupling and population transfer, respectively. A characteristic time of sub-picosecond cross-peaks growth is observed. Ultrafast pump-probe anisotropy studies reveal essentially the same characteristic time for the dipole reorientation. All the experimental data are well modeled in terms of a system undergoing ultrafast population transfer between localized states. Comparison of the experimental observations with simulations reveal a reasonable agreement, although a mechanism including only the fluctuations of the coupling caused by the changes in the dihedral angle of the rotor, is not sufficient to explain the observed ultrafast population transfer.

An ion's perspective on the molecular motions of nanoconfined water: a two-dimensional infrared spectroscopy study

The vibrational population relaxation and hydration shell dynamics of the symmetric tricyanomethanide (TCM) anion are investigated in a sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle as a function of the water pool radius. Two-dimensional infrared (IR) spectroscopy in combination with linear absorption and ultrafast IR pump-probe spectroscopy is utilized in this study. Spectroscopic measurements show that the anion has two bands in the 2160-2175 cm(-1) region, each with its own spectroscopic signatures. Analysis of the vibrational dynamics shows that the two vibrational bands are consistent with the anion located either at the interface or in the water pool. The sensitivity of the TCM anion to the environment allows us to unequivocally monitor the vibrational and hydration dynamics of the anion in those two different environments. A TCM anion located at the interface does not show any significant variation of the vibrational dynamics with the water pool size. On the contrary, the TCM anion inside the water pool exhibits a large and nonlinear variation of the vibrational lifetime and the frequency-frequency correlation time with the pool radius. Moreover, for the solvated anion in water pools of 49 Å in radius (W0 = 30), the vibrational lifetime reaches the values observed for the anion in bulk water while the frequency-frequency correlation time shows a characteristic time higher than that observed in the bulk. In addition, for the first time a model is developed and used to explain the observed nonlinear variation of the spectroscopic observables with the pool size. This model attributes the changes in the vibrational dynamics of the TCM anion in the water pool to the slow and radius-dependent water dynamics present in the confined environment of a reverse micelle.

Quantum Beats and Coherence Decay in Degenerate States Split by Solvation

Coherent dynamics of degenerate quantum states symmetry-broken on the femtosecond timescale is found to exhibit the phenomenon of quantum beats. Frequency-resolved and polarization-selective heterodyned transient grating spectroscopy enabled us to retrieve the oscillation pattern characteristic of the beating in systems undergoing ultrafast dynamical processes. This methodology applies to the general phenomena of coherence dynamics which is important in any ultrafast multidimensional spectroscopy. A particular application to the vibrational spectroscopy of coherence in the degenerate normal modes of the tricyanomethanide anion solvated in water is explored in this study. The relaxation of the cross-polarization transient grating anisotropy is shown to reflect the loss of the vibrational coherence, which is caused by ultrafast dynamics of the water solvation shell.

Differential hydration of tricyanomethanide observed by time resolved vibrational spectroscopy

The degenerate transition corresponding to asymmetric stretches of the D(3h) tricyanomethanide anion, C(CN)(3)(-), in aqueous solution was investigated by linear FTIR spectroscopy, femtosecond pump–probe spectroscopy, and 2D IR spectroscopy. Time resolved vibrational spectroscopy shows that water induces vibrational energy transfer between the degenerate asymmetric stretch modes of tricyanomethanide. The frequency–frequency correlation function and the vibrational energy transfer show two significantly different ultrafast time scales. The system is modeled with molecular dynamics simulations and ab initio calculations. A new model for theoretically describing the vibrational dynamics of a degenerate transition is presented. Microscopic models, where water interacts axially and radially with the ion, are suggested for the transition dipole reorientation mechanism.

Vibrational conical intersections as a mechanism of ultrafast vibrational relaxation

Presenting true crossings of adiabatic potential energy surfaces, conical intersections are a paradigm of ultrafast and efficient electronic relaxation dynamics. The same mechanism is shown to apply also for vibrational conical intersections, which may occur when two high-frequency modes (such as OH stretch vibrations) are coupled to low-frequency modes (such as hydrogen bonding modes). By derivation of a model Hamiltonian and its parametrization for a concrete example, malonaldehyde, the conditions that such conical intersections occur are identified and the consequences for the vibrational dynamics and spectra are demonstrated.

Two-dimensional infrared spectral signature and hydration of the oxalate dianion

Ultrafast vibrational spectra of the aqueous oxalate ion in the region of its carboxylate asymmetric stretch modes show novel relaxation processes. Two-dimensional infrared vibrational echo spectra and the vibrational dynamics obtained from them along with measurements of the anisotropy decay provide a picture in which the localization of the oxalate vibrational excitation onto the carboxylate groups occurs in ~450 fs. Molecular dynamics simulations are used to characterize the vibrational dynamics in terms of dihedral angle motion between the two carboxylate planes and solvation dynamics. The localization of the oxalate vibrational excitation onto the carboxylates is induced by the fluctuations in the carboxylate vibrational frequencies which are shown by theory and experiment to have a similar correlation time as the anisotropy decay.

Identification of arginine residues in peptides by 2D-IR echo spectroscopy

The CN stretching vibrations of the guanidyl group in the arginine dipeptide side chain are examined by two-dimensional infrared spectroscopy. In D(2)O, the spectra display two distinct diagonal peaks. These nearly degenerate modes undergo ultrafast energy transfer. The energy-transfer rate was determined directly from the 2D-IR spectra to be 1/2.1 ps(-1). The cross peaks in 2D-IR arising from the energy transfer provide a definitive identification of arginine in larger proteins. An example of arginine in the transmembrane protein M2, found in influenza viruses, is given.