Fermi Doublet Research Articles

Pressure-induced hydrogen bonding modulating Fermi resonance between fundamental modes in xylitol molecule

Xylitol, as a typical polyol, has a broad range of application prospects. However, the molecular states of xylitol under different environments are rarely reported until now. In this work, the state changes of xylitol molecules under high pressure were analyzed by Raman spectra. A Fermi resonance phenomenon in the fundamental mode of xylitol at 2945 (±0.06) cm−1 and 2955 (±0.41) cm−1 was observed at 0.99 GPa. The Fermi doublets possess the same symmetry and close energy levels, which had not been changed by pressures. However, the high pressure shortened the atomic distances and applied the extra disturbance, providing the necessary conditions for energy transfer. Besides, the Fermi doublets decoupling happened at 4 GPa due to the breaking of hydrogen bonding. This work provides an important reference for studying molecular states and weak interactions of polyols under high pressures.

Tuning the Fermi resonance of pyridine using ethanol molecules

The Fermi resonance (FR) phenomenon is prevalent in infrared and Raman spectroscopy, and it can be observed in a variety of molecules. In particular, pyridine is a compound that has two Fermi doublets: ν1 ∼ ν12 and ν1 + ν6 ∼ ν8. To analyze the effect of environmental changes on the FR, this study first investigated the Raman spectra of pyridine mixed with ethanol at different concentrations. Results indicated that the FR parameters exhibited a nonlinear dependence on the pyridine concentration fractions, and changing the concentration fraction of pyridine led to different hydrogen bond strengths. Second, the interaction mechanism of pyridine-ethanol binary solutions was analyzed by two-dimensional correlation Raman spectroscopy (2DCRS). In addition, high-pressure Raman spectra of a 50% pyridine-ethanol binary solution were measured up to a pressure of 19.65 GPa by a diamond anvil cell technique, and the phase transition of the binary solution occurred at 6.35 GPa. Finally, the impact of ethanol on the FR of pyridine was determined by deducing the FR parameters at different pressures. The turning point at 6.35 GPa was consistent with the Raman frequency–pressure relationships. The results demonstrated that changes in the intensity of ν1 did not affect the FR of ν1 + ν6 ∼ ν8, whereas the undisturbed frequency ν1 still played a role in the FR. When the pressure was compressed to 13.36 GPa, the disappearance of the Raman peaks (ν1 and ν1′) was attributed to the tuning of the molecular symmetry by pressure during the phase transition.

Evaluation of vibrational energies and wave functions of CO2 on a quantum computer

In order to develop a method for evaluating vibrational energies and wave functions of a polyatomic molecule by quantum computing, we introduce the reduced multistate contracted variational quantum eigensolver (RMC-VQE) method, which is a variant of the multistate contracted VQE method [Parrish et al., Phys. Rev. Lett. 122, 230401 (2019)], and apply the RMC-VQE method to a two-mode model of CO2. In the RMC-VQE method, much fewer matrix elements of the Hamiltonian are evaluated on the quantum computer than in the MC-VQE method. By measuring the matrix elements of the Hamiltonian using the quantum computer ibm_kawasaki and diagonalizing the Hamiltonian matrix on a classical computer, we obtain the vibrational energies of the Fermi doublet, which differ from the exact energies obtained using a classical computer by less than 0.1 cm−1. We also obtain accurate vibrational wave functions of the Fermi doublet states.

Raman Spectroscopic Studies on Aqueous Sodium Formate Solutions and DFT Calculations

NaHCOO(aq) and NaDCOO(aq) solutions were measured using Raman spectroscopy from dilute to concentrated solutions at 23 °C in water and heavy water from 50 to 4300 cm−1. A concentrated NaHCOO solution in heavy water was also measured. The Raman band parameters of HCOO−(aq) and DCOO−(aq) such as peak position, full width at half maximum (fwhm), integrated intensities, and depolarization values were determined. From the Raman spectroscopic data, it was concluded that the HCOO−(aq) and DCOO−(aq) symmetry is lower than C2v and probably as low as C1. In contrast to the solution state, tt normalsize tt normalsize {text{HCO}}_{2}^{ - } (tt normalsizettnormalsize {text{DCO}}_{2}^{ - }) possess C2v symmetry in the gas phase and the DFT frequencies are given. DFT frequencies on a cluster of HCOO−/DCOO− with five implicit water molecules in the first sphere and placed in a polarizable continuum deviate not more than 1–2% from the measured ones. In the Raman spectrum in NaHCOO(aq), a band doublet at 2730 cm−1 and 2820 cm−1 occurs instead of a single band. The band doublet is due to Fermi resonance and results from the interaction of the overtone of the bending C–H mode, 2ν6 at 1382 cm−1 and ν1. The undisturbed C–H stretching mode, ν1 amounts to 2785 cm−1. In DCOO−(aq), a Fermi doublet was also observed at 2030.5 and 2116.5 cm−1, and the undisturbed wavenumber position amounts to 2101 cm−1. Furthermore, a solution of HCOO− in D2O showed slightly changed frequencies compared with the ones in water caused by the solvent isotope effect. Ion pairing between Na+ and HCOO− characterizes the Raman spectrum at high solute concentrations which are melt-like enabling direct contact between the ions. A NaHCOO solution with high amounts of LiCl added showed large perturbations of the HCOO− bands especially νsCOO− and δ COO− of HCOO−and revealed a stronger affinity of Li+ toward HCOO−. The ion pairs formed are most likely contact ion pairs between Li+ and HCOO− which have different stoichiometry of Li+: HCOO− such as 1:1 and 2:1.Graphical

Determination of temperature-dependent Fermi resonance in acetonitrile-water binary solution by two-dimensional correlation Raman spectroscopy.

Acetonitrile (AN), as an organic solvent, has a wide range of applications. The C≡N stretching vibration mode (ν2) and the combination mode (ν3 + ν4) are coupled by Fermi resonance (FR). In this work, the phase transition and the interaction mechanism of the 60% AN-water binary solution (AN-Water) were analyzed by calculating FR parameters and two-dimensional correlation Raman spectroscopy (2DCRS). The change in the ν2 band and the base bands ν3 and ν4 caused energy transfer by anharmonic interaction, which led to a change in FR parameters. With a reduced temperature, the energy transfer was caused by microheterogeneity and the energy transfer effect (293-273K), the phase separation (263-233K), and the phase transition of AN (223-173K). The 2DCRS and Gaussian deconvolution provided more information on FR, which revealed the interaction mechanism of the Fermi doublet. The polarity and binding modes of molecules provided a new perspective for analyzing the transmission of electrons and ions in the electrolyte at different temperatures.

Spectroscopic Investigations of 316L Stainless Steel under Simulated Inflammatory Conditions for Implant Applications: The Effect of Tryptophan as Corrosion Inhibitor/Hydrophobicity Marker

In this paper, the conformational changes of tryptophan (Trp) on the corroded 316 L stainless steel (SS) surface obtained under controlled simulated inflammatory conditions have been studied by Raman (RS) and Fourier-transform infrared (FT-IR) spectroscopy methods. The corrosion behavior and protective efficiency of the investigated samples were performed using the potentiodynamic polarization (PDP) technique in phosphate-buffered saline (PBS) solution acidified to pH 3.0 at 37 °C in the presence and absence of 10−2 M Trp, with different immersion times (2 h and 24 h). The amino acid is adsorbed onto the corroded SS surface mainly through the lone electron pair of the nitrogen atom of the indole ring, which adopts a more/less tilted orientation, and the protonated amine group. The visible differences in the intensity of the Fermi doublet upon adsorption of Trp onto the corroded SS surface, which is a sensitive marker of the local environment, suggested that a stronger hydrophobic environment is observed. This may result in an improvement of the corrosion resistance, after 2 h than 24 h of exposure time. The electrochemical results confirm this statement—the inhibition efficiency of Trp, acting as a mixed-type inhibitor, is made drastically higher after a short period of immersion.

Coupling of three intramolecular vibration modes of liquid H2O molecules in the framework of the fluctuation theory of hydrogen bonding.

Vibrational spectra of liquid water contain a wealth of information about its structure and dynamics but there are no generally acknowledged interpretation of their band profiles, unfortunately. We have tried to calculate them taking into account only the coupling of three intramolecular vibrations in the set of H2O molecules with different initial oscillator frequencies and intensities. The matter is that each water molecule forms hydrogen bonds of different strengths; thus the OH stretching band spans several hundreds of wave numbers (the fluctuation theory of hydrogen bonding). This distribution overlaps with the similar band of the first overtone of the HOH bending frequencies thus triggering a Fermi resonance between three vibrations. There were some problems causing some simplifications in previous theoretical modeling of vibrational transitions in condensed water. To solve them we extract the statistical distribution of OH frequencies of H2O molecules directly from the experimental spectra of HOD molecules at the same conditions instead of defining it theoretically. Also the bending overtone is allowed to have non-zero intrinsic intensity when calculating the Fermi resonance. The test calculation of the isotropic component of the Raman spectrum which is most critical for interpretation shows that our algorithm can reproduces the characteristic peculiarities of the experiment. The spectrum consists of three non-Gaussian contours. The overtone of bending vibration, being strengthened by Fermi resonance, makes the greatest contribution to the dominating low-frequency spectrum component that was previously attributed to intermolecular coupling of adjacent OH oscillators by some authors. Further we plan to calculate similar band profiles in the IR and also Raman isotropic and anisotropic spectra of Н2О and D2О molecules within a wide temperature range for their quantitative comparison with experiment.

Real-Time Observation of Fermi Resonances in the S1 State of Phenol.

Fermi resonances in the first electronically excited (S1) state of phenol have been observed in real time. Quantum beats associated with coherent superposition of Fermi resonant eigenstates are manifested as temporal oscillations of the ionization cross sections of which the amplitudes are strongly dependent on the total ionization energy. This indicates that coherently excited eigenstates are effectively decomposed into their zeroth-order states, providing the unique opportunity for the investigation of nonstationary state dynamics in real-time. Energy gaps (Δν̃) of eigenstates within the laser coherence width have been most precisely determined up to date, giving Δν̃ ∼ 3.302 ± 0.001 or 1.655 ± 0.001 cm-1 for the 11/4110b1 or 122/8a1 Fermi doublets, respectively. Dephasing rate suddenly increases as the S1 internal energy becomes above ∼1500 cm-1, revealing the important role of energy randomization dynamics during the H atom tunneling process of phenol in S1.

Raman spectroscopic study of nonlinear modulation on Fermi resonance of acetonitrile by hydrogen-bonding network

Raman spectra of acetonitrile-water mixtures are measured in different acetonitrile concentration fractions. The nitrile stretch (v2) and the combination (v3 + v4) modes are coupled by Fermi resonance. We extract the Fermi resonance parameters and find that the frequency separation shows non-linear dependence as a function of acetonitrile concentration fractions. v2 ~ v3 + v4 Fermi doublets intensity ratio exhibits nonlinearity, which is accelerated with the decreasing of the Fermi coupling strength. The OH stretching region is also investigated in order to reveal the variation of the water structure. Our data show that there are strong relationships between the intensity of ~3225 cm−1 band and the v2~v3 + v4 Fermi resonance. Because the nitrile stretch and Fermi resonance are very environmental sensitive, the nonlinear modulation on Fermi resonance and the non-regular intensity ratio are attributed to the change of water hydrogen-bonding network. The results provide useful structural and spectral insights for the design of new experiments and the molecular structure modeling.

Quantifying conformations of ester vibrational probes with hydrogen-bond-induced Fermi resonances.

Solvatochromic shifts of local vibrational probes report on the strength of the surrounding electric fields and the probe's hydrogen bonding status. Stretching vibrational mode of the ester carbonyl group is a popular solvatochromic reporter used in the studies of peptides and proteins. Small molecules, used to calibrate the response of the vibrational probes, sometimes involve Fermi resonances (FRs) induced by inter-molecular interactions. In the present work, we focus on the scenario where FR does not appear in the infrared spectrum of the ester carbonyl stretching mode in aprotic solvents; however, it is intensified when a hydrogen bond with the reporter is established. When two molecules form hydrogen bonds to the same carbonyl oxygen atom, FR leads to strong hybridization of the involved modes and splitting of the absorption peak. Spectral overlap between the Fermi doublets associated with singly and doubly hydrogen-bonded carbonyl groups significantly complicates quantifying different hydrogen-bonded conformations. We employed a combination of linear and third-order (2DIR) infrared spectroscopy with chemometrics analysis to reveal the individual line shapes and to estimate the occupations of the hydrogen-bonded conformations in methyl acetate, a model small molecule. We identified a hydrogen-bond-induced FR in complexes of methyl acetate with alcohols and water and found that FR is lifted in larger molecules used for control experiments-cholesteryl stearate and methyl cyanoacetate. Applying this methodology to analyze acetonitrile-water solutions revealed that when dissolved in neat water, methyl acetate occupies a single hydrogen-bonding conformation, which is in contrast to the conclusions of previous studies. Our approach can be generally used when FRs prevent direct quantification of the hydrogen bonding status of the vibrational probe.

Raman spectrum of ethane in methane environment

AbstractChanges are investigated in the positions, half‐widths, and intensities of the Q‐branches of the main ethane Raman bands (ν3, 2ν6, 2ν2, 2ν8, and ν1) in the methane/ethane mixture depending on methane concentration at the fixed pressure of 25 bar. It was found that with increasing methane fraction, the above‐mentioned ethane Raman bands, with the exception of ν3, are shifted to the high wavenumbers, and the bands of 2ν8/ν1 Fermi doublet demonstrate a violation of the linear dependence of the intensity on the concentration. The data obtained will be useful for diagnostics of natural gas composition using Raman spectroscopy.

Spectroscopic and non-linear optical studies of two novel optical limiters from dichloroaniline family crystals: 3,4-Dichloroaniline and 3,5-dichloroaniline

Two organic crystals of the isomeric forms of dichloroanilines such as 3, 4-dichloroaniline (3,4-DCA) and 3, 5-dichloroaniline (3,5-DCA) were grown by slow evaporation method and characterized by various analytical techniques. The vibrational normal modes of the samples were theoretically predicted using the scaled quantum mechanical force field procedures with the DFT level calculation and the potential energy distributions of the individual modes were estimated using the normal coordinate analysis. Fermi doublets and Evans holes were identified in the vibrational spectra of samples. The nuclear relaxation contribution to the vibrational polarizabilities and hyperpolarizabilities for the normal modes of the molecules were quantitatively estimated using the DFT method. The results of the calculated NLO responses showed that the vibrational mean contributions to the static polarizabilities and hyperpolarizabilities were smaller than the corresponding electronic contributions for the molecules. The Kurtz and Perry powder SHG efficiencies were measured and both samples have generated the second-harmonics of the fundamentals. The open-aperture Z-scan study results proposed the superior optical limiting property of 3,5-DCA with respect to 3,4-DCA.

Spectral pointillism of enhanced Raman scattering for accessing structural and conformational information on single protein.

In this contribution, we provide new insights on the temporal fluctuations of surface enhanced Raman spectra (SERS) of large single molecules such as proteins. Because they can only fit partly into small active volume, SERS analysis is referred to spectral pointillism where only protein subdomains are shined and the whole protein landscape is built from the dynamics of successive individual spectra. By applying our approach on bovine serum albumin, we show that single protein subdomains are mostly comprised of three distinct amino acids. Surface amino acids such as lysine are preferentially detected in the open form of the protein. The investigation of the tryptophan Fermi doublet in the single protein regime is highly instructive on the protein conformation. We finally demonstrate that spectral pointillism enables to correlate individual amino acids with structural information.

Fermi resonance of two vibrational modes with homogeneously broadened spectral bands

ABSTRACTAnalytical description of the spectra of two coupled vibrational modes in the case of the homogeneous broadening of the interacting bands is proposed. Inter alia, the intrinsic overtone's intensity is taken into account in the course of the analysis of the spectral band shape of the Fermi doublet. General properties of the spectral band at different system parameters are examined. Some experimental spectra are interpreted with our formulas. It is shown that the common practice of decomposition of the observed band into Lorentzian constituents leads to improper values of the interaction parameters when the individual components of the Fermi doublet have different widths.

Intricate packing in the hydrophobic core of barstar through a CH–π interaction

Identification of specific packing interactions within in the hydrophobic core of proteins is important for understanding the integrity of protein structure. Finding such interactions is challenging because few tools allow monitoring of a specific interaction in the presence of several non‐specific forces that hold proteins together. It is important to understand how and when such interactions develop during protein folding. In this study, we have used the intrinsic tryptophan residue, Trp53, as an ultraviolet resonance Raman probe to elucidate the packing interactions in the hydrophobic core of the protein barstar. Barstar is extensively studied for its folding, unfolding and aggregation properties. The Trp53 residue is known to be completely buried in the hydrophobic core of the protein and is used extensively as an intrinsic probe to monitor the folding and unfolding reactions of barstar. A comparison of the resonance Raman cross sections of some bands of Trp53 with those observed for N‐acetyl‐tryptophanoamide in water suggests that Trp53 in barstar is indeed isolated from water. Intensity ratio of the Fermi doublet suggests that Trp53 is surrounded by several aliphatic amino acid residues in corroboration with the crystal structure of barstar. Importantly, we show that the side chain of Trp53 is involved in a unique CH–π interaction with CH groups of Phe56 as well as a steric interaction with the methyl group of Ile5. Copyright © 2014 John Wiley & Sons, Ltd.

Effects of atmospheric relative humidity on Stratum Corneum structure at the molecular level: ex vivo Raman spectroscopy analysis

Skin hydration plays an important role in the optimal physical properties and physiological functions of the skin. Despite the advancements in the last decade, dry skin remains the most common characteristic of human skin disorders. Thus, it is important to understand the effect of hydration on Stratum Corneum (SC) components. In this respect, our interest consists in correlating the variations of unbound and bound water content in the SC with structural and organizational changes in lipids and proteins using a non-invasive technique: Raman spectroscopy. Raman spectra were acquired on human SC at different relative humidity (RH) levels (4-75%). The content of different types of water, bound and free, was measured using the second derivative and curve fitting of the Raman bands in the range of 3100-3700 cm(-1). Changes in lipidic order were evaluated using νC-C and νC-H. To analyze the effect of RH on the protein structure, we examined in the Amide I region, the Fermi doublet of tyrosine, and the νasymCH3 vibration. The contributions of totally bound water were found not to vary with humidity, while partially bound water varied with three different rates. Unbound water increased greatly when all sites for bound water were saturated. Lipid organization as well as protein deployment was found to be optimal at intermediate RH values (around 60%), which correspond to the maximum of SC water binding capacity. This analysis highlights the relationship between bound water, the SC barrier state and the protein structure and elucidates the optimal conditions. Moreover, our results showed that increased content of unbound water in the SC induces disorder in the structures of lipids and proteins.

The effect of an anti-hydrogen bond on Fermi resonance: A Raman spectroscopic study of the Fermi doublet ν1−ν12 of liquid pyridine

The effects of an anti-hydrogen bond on the ν1−ν12 Fermi resonance (FR) of pyridine are experimentally investigated by using Raman scattering spectroscopy. Three systems, pyridine/water, pyridine/formamide, and pyridine/carbon tetrachloride, provide varying degrees of strength for the diluent-pyridine anti-hydrogen bond complex. Water forms a stronger anti-hydrogen bond with pyridine than with formamide, and in the case of adding non-polar solvent carbon tetrachloride, which is neither a hydrogen bond donor nor an acceptor and incapable of forming a hydrogen bond with pyridine, the intermolecular distance of pyridine will increase and the interaction of pyridine molecules will reduce. The dilution studies are performed on the three systems. Comparing with the values of the Fermi coupling coefficient W of the ring breathing mode ν1 and triangle mode ν12 of pyridine at different volume concentrations, which are calculated according to the Bertran equations, in three systems, we find that the solution with the strongest anti-hydrogen bond, water, shows the fastest change in the ν1−ν12 Fermi coupling coefficient W with the volume concentration varying, followed by the formamide and carbon tetrachloride solutions. These results suggest that the stronger anti-hydrogen bond-forming effect will cause a greater reduction in the strength of the ν1−ν12 FR of pyridine. According to the mechanism of the formation of an anti-hydrogen bond in the complexes and the FR theory, a qualitative explanation for the anti-hydrogen bond effect in reducing the strength of the ν1−ν12 FR of pyridine is given.

Correlation of TrpGly and GlyTrp Rotamer Structure with W7 and W10 UV Resonance Raman Modes and Fluorescence Emission Shifts

Tryptophyl glycine (TrpGly) and glycyl tryptophan (GlyTrp) dipeptides at pH 5.5 and pH 9.3 show a pattern of fluorescence emission shifts with the TrpGly zwitterion emission solely blue shifted. This pattern is matched by shifts in the UV resonance Raman (UVRR) W10 band position and the W7 Fermi doublet band ratio. Ab initio calculations show that the 1340 cm−1 band of the W7 doublet is composed of three modes, two of which determine the W7 band ratios for the dipeptides. Molecular dynamics simulations show that the dipeptides take on two conformations: one with the peptide backbone extended; one with the backbone curled over the indole. The dihedral angle critical to these conformations is χ 1 and takes on three discrete values. Only the TrpGly zwitterion spends an appreciable amount of time in the extended backbone conformation as this is stabilized by two hydrogen bonds with the terminal amine cation. According to a Stark effect model, a positive charge near the pyrrole keeps the 1La transition at high energy, limiting fluorescence emission red shift, as observed for the TrpGly zwitterion. The hydrogen bond stabilized backbone provides a rationale for the Cmethylene-Cα-Ccarbonyl W10 symmetric stretch that is unique to the TrpGly zwitterion.

UV resonance Raman study of TrpZip2 and related peptides: π-π interactions of tryptophan.

Aromatic interactions are important stabilizing forces in proteins but are difficult to detect in the absence of high-resolution structures. Ultraviolet resonance Raman spectroscopy is used to probe the vibrational signatures of aromatic interactions in TrpZip2, a synthetic β-hairpin peptide that is stabilized by edge-to-face and face-to-face tryptophan π-π interactions. The vibrational markers of isolated edge-to-face π-π interactions are investigated in the related β-hairpin peptide W2W11. The bands that comprise the Fermi doublet exhibit systematic shifts in position and intensity for TrpZip2 and W2W11 relative to the model peptide, W2W9, which does not form aromatic interactions. Additionally, hypochromism of the Bb absorption band of tryptophan in TrpZip2 leads to a decrease in the relative Raman cross-sections of Bb-coupled Raman bands. These results reveal spectral markers for stabilizing tryptophan π-π interactions and indicate that ultraviolet resonance Raman may be an important tool for the characterization of these biological forces.

Raman spectroscopy study on the [formula omitted] Fermi resonance of liquid carbon disulfide in binary solutions: Effect of the weak hydrogen bond formation on the Fermi resonance

We have measured the Raman spectra of liquid CS2 at different volume concentrations in CHCl3 and CH2Cl2 solutions. With decreasing the volume concentration of CS2, a noticeable growth in the 2ν2 band frequency was observed, while the ν1 band location remained practically unchanged. This asymmetric wavenumber shift phenomenon of the Fermi doublet ν1 and 2ν2 of CS2 has been ascribed to weak, non-conventional hydrogen bonds formed between the CS2 and the solvent molecules. These weak hydrogen bonds were also responsible for significant decreases in the C–H bond symmetric stretching vibration band frequencies of CHCl3 and CH2Cl2. The values of the ν1-2ν2 FR parameters of CS2 in CH2Cl2 and CHCl3 at different volume concentrations were calculated according to the FR theory. The magnitude of the FR coupling coefficient W of CS2 increases upon dilution with CH2Cl2 and CHCl3, indicating that the vibrational anharmonicity is relatively sensitive to variations in the weak hydrogen bonding. Compared with the changing tendencies of Fermi coupling coefficient W of CS2 in CH2Cl2 and CHCl3 at different volume concentrations, we discussed the effect of the weak hydrogen bond formation on the FR and the asymmetric wavenumber shift phenomenon of the Fermi doublet ν1 and 2ν2 of CS2.