Stretch Mode Research Articles

Stationary and Time-Dependent Carbon Monoxide Stretching Mode Features in Carboxy Myoglobin: A Theoretical-Computational Reappraisal.

The stationary and time-dependent infrared spectrum (IR) of the CO stretching mode (νCO) in carboxymyoglobin (MbCO), a longstanding problem of biophysical chemistry, has been modeled through a theoretical-computational method specifically designed for simulating quantum observables in complex atomic-molecular systems and based on a combined application of long time scale molecular dynamics simulations and quantum-chemical calculations. This study is basically focused on two aspects: (i) the origin of the stationary IR substates (termed as A0, A1, and A3) and (ii) the modeling and the interpretation of the νCO energy relaxation. The results, strengthened by a more than satisfactory agreement with the experimental data, concisely indicate that (i) the conformational His64-FeCO relevant substates, i.e., characterized by the formation-disruption of the H-bond between the above moieties, are the main responsible of the presence of two distinct and well separated (A0 and A1/A3) spectroscopic regions; (ii) the characteristic bimodal shape of the A1/A3 spectral region, according to our model, is the result of the fluctuation of the electric field pattern as provided by the protein-solvent framework perturbing the bound His64-CO-Heme complex; and (iii) the electric field pattern, in conjunction with the relatively high density of MbCO vibrational states, is also the main determinant of the νCO energy relaxation, characterizing its kinetic efficiency.

Flexible boundary layer using exchange for embedding theories. II. QM/MM dynamics of the hydrated electron.

The FlexiBLE embedding method introduced in Paper I [Z. Shen and W. J. Glover, J. Chem. Phys. 155, 224112 (2021)] is applied to explore the structure and dynamics of the aqueous solvated electron at an all-electron density functional theory Quantum Mechanics/Molecular Mechanics level. Compared to a one-electron mixed quantum/classical description, we find the dynamics of the many-electron model of the hydrated electron exhibits enhanced coupling to water OH stretch modes. Natural bond orbital analysis reveals this coupling is due to significant population of water OH σ* orbitals, reaching 20%. Based on this, we develop a minimal frontier orbital picture of the hydrated electron involving a cavity orbital and important coupling to 4-5 coordinating OH σ* orbitals. Implications for the interpretation of the spectroscopy of this interesting species are discussed.

Flexural stress effect on mechanical and mechanochemical properties of soda lime silicate glass surface

AbstractAs a means to elucidate the mechanical stress effect on the durability of soda lime silicate (SLS) float glass, a thin glass plate under flexural stress was investigated with X‐ray photoelectron spectroscopy (XPS), specular reflectance infrared (SR‐IR) spectroscopy, nanoindentation, and tribo‐testing. A lab‐built four‐point bending rig was employed to create compressive or tensile stress (around 40 MPa) on the air‐side surface of SLS glass. XPS analysis showed that electric field‐induced sodium ion migration is greatly enhanced in both compressive and tensile stress surfaces. The SR‐IR analysis of the Si‐O‐Si stretch mode revealed that the structural distortion of the silicate network appears to be larger under compressive stress than tensile stress. The elastic and plastic responses of the SLS surface to nanoindentation were significantly altered under the flexural stress conditions even though the magnitude of the flexural stress was less than 0.7% of the applied indentation stress. Compared to the stress‐free surface, the resistance to mechanochemical wear at 90% relative humidity deteriorated under the compressive stress condition, while it just became more scattered under the tensile stress condition. Even though the applied flexural stress was very small, its impact on chemical and structural properties could be surprisingly large. Combining all results in this study and previously published works suggested that the changes observed in nanoindentation and mechanochemical wear behaviors may be associated with the strain in the Si‐O bonds of the silicate network.

Absolute Absorption Cross Section and Orientation of Dangling OH Bonds in Water Ice

Abstract The absolute absorption cross section of dangling OH bonds in water ice, a free OH stretch mode by three-coordinated surface water molecules, is derived experimentally as 1.0 ± 0.2 × 10−18 cm2 at 3696 cm−1 for amorphous water at 90 K using infrared multiple-angle incidence resolution spectrometry (IR–MAIRS). The integrated absorption cross section (band strength) of the dangling OH bond at 90 K (1.4 ± 0.3 × 10−17 cm molecule−1 at 3710–3680 cm−1) is found to be more than 1 order of magnitude smaller than those in bulk ice or liquid water. This indicates that a lack of hydrogen-bonding significantly decreases the band strength of dangling OH bonds. The present study also provides average molecular orientations of dangling OH bonds at 10 K and 90 K, because both the surface-parallel (in-plane) and surface-perpendicular (out-of-plane) vibration spectra of dangling OH bonds are quantitatively measured by IR–MAIRS. The intensity ratio of the dangling-OH peaks between in-plane to out-of-plane spectra shows the isotropic nature (random orientation) of the two- and three-coordinated dangling OH bonds in microporous amorphous water prepared at 10 K; however, the three-coordinated dangling OH bonds in nonporous amorphous water prepared at 90 K are dominantly located at the top ice surface and oriented perpendicular to it. These findings provide fundamental insights into the relationship between the structure and optical properties of ice surfaces, and aid quantitative understanding of the surface structure of interstellar ices and their laboratory analogs.

Understanding the Surface Characteristics of Biochar and Its Catalytic Activity for the Hydrodeoxygenation of Guaiacol

Biochar (BCR) was obtained from the pyrolysis of a palm-oil-empty fruit bunch at 773 K for 2 h and used as a catalyst for the hydrodeoxygenation (HDO) of guaiacol (GUA) as a bio-oil model compound. Brunauer–Emmet–Teller surface area analysis, NH3 and CO2-temperature-programmed desorption, scanning electron microscope–dispersive X-ray spectroscopy, CHN analysis and X-ray fluorescence spectroscopy suggested that macroporous and mesoporous structures were formed in BCR with a co-presence of hydrophilic and hydrophobic sites and acid–base behavior. A combination of infrared, Raman and inelastic neutron scattering (INS) was carried out to achieve a complete vibrational assignment of BCR. The CH–OH ratio in BCR is ~5, showing that the hydroxyl functional groups are a minority species. There was no evidence for any aromatic C–H stretch modes in the infrared, but they are clearly seen in the INS and are the majority species, with a ratio of sp3–CH:sp2–CH of 1:1.3. The hydrogen bound to sp2–C is largely present as isolated C–H bonds, rather than adjacent C–H bonds. The Raman spectrum shows the characteristic G band (ideal graphitic lattice) and three D bands (disordered graphitic lattice, amorphous carbon, and defective graphitic lattice) of sp2 carbons. Adsorbed water in BCR is present as disordered layers on the surface rather than trapped in voids in the material and could be removed easily by drying prior to catalysis. Catalytic testing demonstrated that BCR was able to catalyze the HDO of GUA, yielding phenol and cresols as the major products. Phenol was produced both from the direct demethoxylation of GUA, as well as through the demethylation pathway via the formation of catechol as the intermediate followed by deoxygenation.

Disorder in P3HT Nanoparticles Probed by Optical Spectroscopy on P3HT-b-PEG Micelles.

We employ photoluminescence (PL) spectroscopy on individual nanoscale aggregates of the conjugated polymer poly(3-hexylthiophene), P3HT, at room temperature (RT) and at low temperature (LT) (1.5 K), to unravel different levels of structural and electronic disorder within P3HT nanoparticles. The aggregates are prepared by self-assembly of the block copolymer P3HT-block-poly(ethylene glycol) (P3HT-b-PEG) into micelles, with the P3HT aggregates constituting the micelles’ core. Irrespective of temperature, we find from the intensity ratio between the 0–1 and 0–0 peaks in the PL spectra that the P3HT aggregates are of H-type nature, as expected from π-stacked conjugated thiophene backbones. Moreover, the distributions of the PL peak ratios demonstrate a large variation of disorder between micelles (inter-aggregate disorder) and within individual aggregates (intra-aggregate disorder). Upon cooling from RT to LT, the PL spectra red-shift by 550 cm–1, and the energy of the (effective) carbon-bond stretch mode is reduced by 100 cm–1. These spectral changes indicate that the P3HT backbone in the P3HT-b-PEG copolymer does not fully planarize before aggregation at RT and that upon cooling, partial planarization occurs. This intra-chain torsional disorder is ultimately responsible for the intra- and inter-aggregate disorder. These findings are supported by temperature-dependent absorption spectra on thin P3HT films. The interplay between intra-chain, intra-aggregate, and inter-aggregate disorder is key for the bulk photophysical properties of nanoparticles based on conjugated polymers, for example, in hierarchical (super-) structures. Ultimately, these properties determine the usefulness of such structures in hybrid organic–inorganic materials, for example, in (bio-)sensing and optoelectronics applications.

Vibrational spectroscopy analysis of silica and silicate glass networks

AbstractVibrational spectroscopy has been widely used to investigate various structural aspects of the glass network, and there are a plethora of papers reporting subtle but consistent changes in infrared and Raman spectral features of glass upon alterations of glass compositions, thermal histories, mechanical stresses, or surface treatments. However, interpretations of such spectral features are still obscured due to the lack of well‐established physical principles accurately describing vibrational modes of the non‐crystalline glass network. Due to the non‐equilibrium nature of the glass network, three‐dimensionally connected without any long‐range orders, vibrational spectral features of glass cannot be interpreted using the analogy with those of isolated molecular moieties or crystalline counterparts. This feature article explains why such comparisons are outdated and describes the recent advances made from theoretical calculations of vibrational spectral features of amorphous networks or comparisons of computational results with experimental data. For the interpretation of vibrational spectral features of silica and silicate glasses, the following empirical relationships are suggested: (i) the intensity‐weighted peak position of the Si‐O‐Si stretch mode negatively correlates with the weighted average of the Si‐O bond length distribution, and (ii) the broad band of the Si‐O‐Si bending mode negatively correlates with the Si‐O‐Si bond angle distribution. Selected examples of vibrational spectroscopic imaging of surface defects are discussed to deliberate the implication of these findings in the structure‐property relationship of silica and silicate glass materials. Unanswered questions and continuing research challenges are identified.

CD Stretching Modes are Sensitive to the Microenvironment in Ionic Liquids.

Knowledge of the structure of the electrical double layer in ionic liquids (IL) is crucial for their applications in electrochemical technologies. We report the synthesis and applicability of an imidazolium‐based amphiphilic ionic liquid with a perdeuterated alkyl chain for studies of electric potential‐dependent rearrangements, and changes in the microenvironment in a monolayer on a Au(111) surface. Electrochemical measurements show two states of the organization of ions on the electrode surface. In situ IR spectroscopy shows that the alkyl chains in imidazolium cations change their orientation depending on the adsorption state. The methylene‐d 2 stretching modes in the perdeuterated IL display a reversible, potential‐dependent appearance of a new band. The presence of this mode also depends on the anion in the IL. Supported by quantum chemical calculations, this new mode is assigned to a second ν as(CD2) band in alkyl‐chain fragments embedded in a polar environment of the anions/solvent present in the vicinity of the imidazolium cation and electrode. It is a measure of the potential‐dependent segregation between polar and nonpolar environments in the layers of an IL closest to the electrode.

Probing Hydrogen-Bonding Interactions within Phenol-Benzimidazole Proton-Coupled Electron Transfer Model Complexes with Cryogenic Ion Vibrational Spectroscopy.

Hydrogen-bonding interactions within a series of phenol-benzimidazole model proton-coupled electron transfer (PCET) dyad complexes are characterized using cryogenic ion vibrational spectroscopy. A highly red-shifted and surprisingly broad (>1000 cm-1) transition is observed in one of the models and assigned to the phenolic OH stretch strongly H-bonded to the N(3) benzimidazole atom. The breadth is attributed to a combination of anharmonic Fermi-resonance coupling between the OH stretch and background doorway states involving OH bending modes and strong coupling of the OH stretch frequency to structural deformations along the proton-transfer coordinate accessible at the vibrational zero-point level. The other models show unexpected protonation of the benzimidazole group upon electrospray ionization instead of at more basic remote amine/amide groups. This leads to the formation of HO-+HN(3) H-bond motifs that are much weaker than the OH-N(3) H-bond arrangement. H-bonding between the N(1)H+ benzimidazole group and the carbonyl on the tyrosine backbone is the stronger and preferred interaction in these complexes. The results show that conjugation effects, secondary H-bond interactions, and H-bond soft modes strongly influence the OH-N(3) interaction and highlight the importance of the direct monitoring of proton stretch transitions in characterizing the proton-transfer reaction coordinate in PCET systems.

Interfacial Vibrational Spectroscopy of the Water Bending Mode on Ice Ih

We study the molecular-level properties of the single-crystal ice Ih surface using interface-specific sum frequency generation spectroscopy. We probe the water vibrational bend region around 1650 cm–1 of the basal plane of hexagonal ice to understand the interfacial structure from vibrational properties. As opposed to the stretch mode of ice, the bending mode response depends very weakly on temperature. The large line width of the bending mode response, relative to the response on water, is inconsistent with inhomogeneous broadening and points to ultrafast pure dephasing. The bending mode of ice provides an excellent means to study adsorbate–ice interactions and understand differences in ice and water reactivity.

Effects of hydrophobic solute on water normal modes

In this work, we examine the effects of methane, on the normal modes of water. We find methane has a weaker influence on water normal modes. We estimate the vibrational density of states and the infrared spectral density. We decompose these modes based on different vibrational characters. We observe a general decrease in intensity throughout the water stretch region in the methane-water system compared to the bulk water data. This lower intensity reflects the reduction of the number of average water molecules in the methane-water system. The stretch-bend decomposition reflects a pronounced coupling between the methane asymmetric stretch mode and the water symmetric stretch mode. We examine the methane-water data in terms of the symmetry of the central water molecule’s vibrations and find that asymmetric modes do not contribute. We also find that the vibrational modes having non-zero contributions from methane molecule are extremely localized in nature.

Solvation Structure around Li+ Ions in Organic Carbonate Electrolytes: Spacer-Free Thin Cell IR Spectroscopy.

Organic carbonate electrolytes are widely used materials for lithium-ion batteries. However, detailed solvation structures and solvent coordination numbers (CNs) of lithium cations in such solutions have not been accurately described nor determined yet. Because transmission-type IR spectroscopy is not of use for measuring the carbonyl stretch modes of electrolytes due to their absorption saturation problem, we here show that simple spacer-free thin cell IR spectroscopy can provide quantitative information on the number of solvating carbonate molecules around each lithium ion. We could estimate the solvent (carbonate) CNs of lithium ions in dimethyl carbonate, ethyl methyl carbonate, diethyl carbonate, propylene carbonate, and butylene carbonate over a wide range of lithium salt concentrations accurately, and they are compared with the previous results obtained with attenuated total reflection IR spectroscopy technique. We anticipate that our spacer-free thin cell approach will potentially be used to investigate the solvation dynamics, chemical exchange process, and vibrational energy transfers between solvating carbonate molecules in lithium salt electrolytes when combined with time-resolved IR spectroscopy.

Why the CC Stretch in HCC Is So Anharmonic

The marked anharmonicity of the CC stretching mode in the ethynyl radical (C2H) is investigated in terms of a vibronic coupling model. It is demonstrated that the large difference between the harmonic frequency and the fundamental level (about 5-10 times that for triple-bond stretches in the related species HCCH, HCN, HNC and CN) can be attributed to the well-known vibronic interaction between the X̃2Σ+ and Ã2Π states of CCH. Although the mode has σ symmetry and it is the perturbations of π symmetry that mix the two electronic states, a combination of large intrinsic coupling strength, modest energy gap, and-most importantly-the strong tuning of the gap energy by the CC stretch mode leads to a profound vibronic influence on parts of the anharmonic force field that sample the CC stretch. Finally, calculations of the force field for the X̃2Σ+ state with different flavors of coupled-cluster (CC) theory provide insight and underscore an intrinsic advantage of equation-of-motion CC (EOM-CC) methods.

Substituent Effects on the Vibrational Properties of the CN Stretch Mode of Aromatic Nitriles: IR Probes Useful for Time-resolved IR Spectroscopy.

Developing ideal IR probes is essential to understand the structure and dynamics of biomolecules with time-resolved IR spectroscopies and imaging techniques. Especially, nitrile (CN) group has recently been proposed to serve as IR probes of the local environment of proteins. Herein, we investigated the effect of a substituent on the vibrational properties of the benzonitrile. The electron-donating and withdrawing character of p-substituent on benzonitrile are expected to modulate the vibrational frequency, molar extinction coefficient, and vibrational lifetime of CN probe. FT-IR revealed the positive correlation between electron-donating character and the molar extinction coefficient of CN stretch mode. Infrared pump-probe (IR-PP) measurements showed that the vibrational lifetime of CN stretch mode exhibits a relatively weak correlation with the electron-donating strength. Among the investigated samples, 4-dimethylamino benzonitrile with the strongest electron-donating strength shows enhanced absorption and extended vibrational lifetime. Utilizing substituent effects will be a practical strategy to improve the performance of the IR probe.

Two-Dimensional Adiabatic Model for Calculating Progressions Resulting from Stretch–Rock Coupling in Vibrational Spectra of Anion–Water Complexes

Several anion-water dimers feature a distinct progression in the OH stretch region of their vibrational spectra. This progression arises from strong anharmonic couplings between the OH stretch and low-frequency intermolecular modes. In this work, we introduce a two-dimensional adiabatic model accounting explicitly for the water and anion rock degrees of freedom and use it to calculate the vibrational spectra of HCO2-·(H2O) and NO3-·(H2O). The spectra calculated by using this model are in excellent agreement with experiment, in terms of both peak spacings and lengths of the progressions, and represent a substantial improvement over earlier models.

Elucidating the Mechanism of Ambient-Temperature Aldol Condensation of Acetaldehyde on Ceria.

Using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and density functional theory (DFT) calculations, we conclusively demonstrate that acetaldehyde (AcH) undergoes aldol condensation when flown over ceria octahedral nanoparticles, and the reaction is desorption-limited at ambient temperature. trans-Crotonaldehyde (CrH) is the predominant product whose coverage builds up on the catalyst with time on stream. The proposed mechanism on CeO2(111) proceeds via AcH enolization (i.e., α C–H bond scission), C–C coupling, and further enolization and dehydroxylation of the aldol adduct, 3-hydroxybutanal, to yield trans-CrH. The mechanism with its DFT-calculated parameters is consistent with reactivity at ambient temperature and with the kinetic behavior of the aldol condensation of AcH reported on other oxides. The slightly less stable cis-CrH can be produced by the same mechanism depending on how the enolate and AcH are positioned with respect to each other in C–C coupling. All vibrational modes in DRIFTS are identified with AcH or trans-CrH, except for a feature at 1620 cm–1 that is more intense relative to the other bands on the partially reduced ceria sample than on the oxidized sample. It is identified to be the C=C stretch mode of CH3CHOHCHCHO adsorbed on an oxygen vacancy. It constitutes a deep energy minimum, rendering oxygen vacancies an inactive site for CrH formation under given conditions.

Molecular and micro-scale heterogeneities in Raman modes of a relaxing polymer glass

We have used Raman spectroscopy to study relaxation dynamics at two different length scales, molecular level and micro-scale in order to probe the presence of cooperative rearranging regions in a polymer glass. Response to slow thermal cycles and fast quench through the glass transition temperature (T g) is analyzed for film and unprocessed forms of polyvinyl acetate (PVAc). In PVAc film, enhanced disorder and molecular mobility lead to peak broadening by about a factor of 10 compared to unprocessed PVAc. Thermal cycles (10 K min−1) produce hysteresis in integrated Raman peak intensity (loop area ). values of film are two orders of magnitude more than unprocessed, indicating more configurational mosaics with higher interfacial energy dissipations. Ageing after 60 K min−1 quench manifests as heterogeneous molecular dynamics of film Raman modes with significant peak-width variations, differentiating high mobility and low mobility modes. Two-dimensional mapping of film Raman modes after quench reveal micro-scale clusters of average size ≈250 molecules having fractal boundaries with fractal dimension d f = 1.5, resembling d f of percolation clusters below percolation threshold. During thermal cycling and relaxation after a quench, cooperative segmental dynamics with large correlations between skeletal C–C stretch and side branch modes is observed. The observations are analyzed in the context of the random first order transition theory of glasses, which attributes heterogeneous relaxations in glasses to the presence of clusters of variable configurational states.

Vibrational spectroscopy of uranium tetrafluoride hydrates

Uranium tetrafluoride (UF4) is an important intermediate in the production of UF6 and nuclear fuel. Historical characterization of UF4 with Raman spectroscopy was plagued with ambiguity until the first accurate Raman spectrum was published by our group in 2016. Although generally considered to be relatively stable, UF4 can hydrolyze to form numerous UF4 hydrates that may play a role in future uranium waste forms. In contrast to anhydrous UF4, the hydrates, with their OH stretch and HOH bending modes, can be spectroscopically characterized by the type and degree of water bonding in the crystal lattice, which can yield additional information about their crystal structure. Herein, vibrational spectroscopy (Raman and infrared) was used to characterize three different UF4 hydrates: UF4(H2O)0.33, U3F12(H2O), and UF4(H2O)2.5. Spectra show the different hydrates vary in the number of observed bands, full-width half-maximum of the bands, and band intensity. These differences are due to varying interactions between the OH stretch and HOH bending modes with UF4 and the polymeric UF4 structure in the crystal lattice. These vibrational data, in combination with spectral fitting and crystallographic structures measured with powder X-ray diffraction and single crystal X-ray diffraction, provide unique details on the location of water molecules in the crystal lattice of hydrated UF4, and provide an interesting contrast to the vibrational spectra of anhydrous UF4.

Time evolution of CO2 ro-vibrational excitation in a nanosecond discharge measured with laser absorption spectroscopy

CO2 dissociation stimulated by vibrational excitation in non-equilibrium discharges has drawn lots of attention. Nanosecond (ns) discharges are known for their highly non-equilibrium conditions. It is therefore of interest to investigate the CO2 excitation in such discharges. In this paper, we demonstrate the ability for monitoring the time evolution of CO2 ro-vibrational excitation with a well-selected wavelength window around 2289.0 cm−1 and a single continuous-wave quantum cascade laser with both high accuracy and temporal resolution. The rotational and vibrational temperatures for both the symmetric and the asymmetric modes of CO2 in the afterglow of CO2 + He ns-discharge were measured with a temporal resolution of 1.5 μs. The non-thermal feature and the preferential excitation of the asymmetric stretch mode of CO2 were experimentally observed, with a peak temperature of Tv 3, max = 966 ± 1.5 K, Tv 1,2, max = 438.4 ± 1.2 K and T rot = 334.6 ± 0.6 K reached at 3 μs after the nanosecond pulse. In the following relaxation process, an exponential decay with a time constant of 69 μs was observed for the asymmetric stretch (001) state, consistent with the dominant deexcitation mechanism due to VT transfer with He and deexcitation on the wall. Furthermore, a synchronous oscillation of the gas temperature and the total pressure was also observed and can be explained by a two-line thermometry and an adiabatic process. The period of the oscillation and its dependence on the gas components is consistent with a standing acoustic wave excited by the ns-discharge.

2D Vibrational Exciton Nanoimaging of Domain Formation in Self-Assembled Monolayers.

Order, disorder, and domains affect many of the functional properties in self-assembled monolayers (SAMs). However, carrier transport, wettability, and chemical reactivity are often associated with collective effects, where conventional imaging techniques have limited sensitivity to the underlying intermolecular coupling. Here we demonstrate vibrational excitons as a molecular ruler of intermolecular wave function delocalization and nanodomain size in SAMs. In the model system of a 4-nitrothiophenol (4-NTP) SAM on gold, we resolve coupling-induced peak shifts of the nitro symmetric stretch mode with full spatio-spectral infrared scattering scanning near-field optical microscopy. From modeling of the underlying 2D Hamiltonian, we infer domain sizes and their distribution ranging from 3 to 12 nm across a field of view on the micrometer scale. This approach of vibrational exciton nanoimaging is generally applicable to study structural phases and domains in SAMs and other molecular interfaces.